Let's also look at a slight rephrasing of the question: how can a society be stable when overpowered wizards can kill on a whim? This perspective shift is useful, since a stable society wouldn't have no magical murder, but it would be rare enough that most people could go about their daily lives, just as in our own world. How rare depends on what sort of characters and world do you want to explore, anything from a world where magical murder doesn't show up as a concern in the story to one where it's a primary theme and its affects on individuals and society is a driving force of the story (though you can get the latter even when magical murder is quite rare). Where the world falls on this spectrum depends on stabilizing factors (with no single deciding factor). While much of the below isn't explicitly cast in terms of costs, benefits and incentives, they can be identified in the list.
Generic
Some factors will exist in any world. These aren't stated as rules of the world so much as their occurrence is natural and prevalent, such as in the attitudes (and thus behaviors) of folk. The attitudes of mundanes and wizards will affect each other, which can provide additional reinforcing stabilizing (and occasionally destabilizing) affects.
Natural Consequences
Psychological Consequences
Many people, fortunately, simply have a hard time killing others. Doing so severely impacts their psyche, so they avoid it. It can take extreme circumstances to overcome this.
This only works if the other is seen as a person. Wizards might view themselves as superior to others to the point that they consider others to be a lower order, which would be a destabilizing factor (see Wizard Attitudes below).
Mundanes Assemble
If the mundanes outnumber the wizards and wizards become a large problem for society, the mundanes will band together to attack the wizards. If the wizards are so powerful that the armies are unlikely to win, it might still take long enough for a wizard to destroy an army that they'd rather spend their time on their Other Concerns (see below). It could be that there's a tipping point in the army size, beyond which a wizard isn't likely to prevail. Even if they can teleport away, they may have to leave behind their valuable equipment. This factor involves periodic instability, though it might not happen during the time of the story.
The above factor may stabilize into a condition where wizards are attacked on sight. Wizards might thus have to take care in concealing their powers to the point of not using magic. From the people's perspective, if someone is killed by magical means and you don't have a way of determining who did it, you might not care exactly who pays the price as long as someone does. This can be a destabilizing factor as not only wizards will suffer.
Even if it doesn't come to a physical fight, wizards will likely have to deal with society. This will temper their interactions.
Demographics
The ratio of mundanes to wizards greatly impacts instability caused by magical murder. If most mundanes go their entire lives without encountering a wizard, magical murder won't be a social problem. For those rare times that mundanes encounter a wizard, their behavior will likely be such that they won't give the wizard cause.
If wizards are common, or even a majority, it can be bad news for mundanes, for even if you aren't the target, you might become collateral damage (fireballs having an area of effect).
Mundane Attitudes
How mundanes view and interact with wizards will naturally contribute greatly to stability.
Fear
Mundane folk will do just about anything to avoid offending wizards who can easily kill them. Not giving wizards reasons to kill off folk around them will go a long way towards making it a rare occurrence. Just how fearful mundanes are sets the tone of the world. It might be a world that is terrible to live in for mundanes, but is still stable.
Mundane fear can drive wizards to isolation. This could motivate wizards to not give mundanes cause to fear. Alternatively, if wizards aren't concerned with being excluded from mundane society but a wizard is driven to contact mundanes, it will likely be out of need. The wizard can't then wantonly kill whomever they come in contact with, else their need won't be met. The wizard may get angry at times, but will largely keep that anger in check. Isolation results in various characters of wizard, such as great and powerful, or mysterious and reserved, or kind (so a mundane may not recognize them as a wizard at first).
Respect
If other factors make wizard perpetrated death rare and it's also perceived to be rare by mundanes, they will still treat wizards with respect because of wizards' great abilities.
When treated with respect, wizards will likely respond with respect.
Wizard Attitudes
Either due to training or as a response to experience, the attitudes of a wizard are at the core of the question.
Mental Disorders
A wizard's inclination to kill someone without reason is a destabilizing factor. The more rare that malignant mental disorders are among wizards, the more stable the society. This also ties in with demographics, as prevalence of these disorders can be offset by having fewer wizards.
Values
Any value wizards place on mundanes will be much more variable, less a matter of natural incentives than of (wizard) education, (wizard) social norms, and individual philosophies. These may be less satisfactory, as they seem more arbitrary and due to the finger of the author (and may need to be stated, rather than appearing like background radiation). However, you might be able to connect these with another factor so it doesn't feel so arbitrary.
Wizards might take a paternalistic stance, viewing mundanes as being akin to children in terms of power, and thus something to be protected (even from themselves). As with children, while wizards might get angry and even punish them, most wizards won't go so far as to cause any permanent, debilitating damage.
Even without paternalism, not all wizards would use powerful magic, or even any magic, to deal with a blundering mundane if it's not necessary. It might be viewed as overkill, which an economical wizard would avoid, or excessive force. It all comes down to what a wizard considers a measured response, and whether they have the presence of mind to give it.
Wizards might not much care about mundanes and what they do in a particular interaction (see Other Concerns). Consequently, instead of teleporting something inside a mundane and killing them, a wizard's reflexive reaction might be to teleport the mundane outside the area, such as to the street, a dung heap, a nearby lake or river, or a desert island. This can even happen if wizards view mundanes as lower orders, just as you might wave away a moth that's flying around you. Of course, some wizards might respond with a magical swat.
At an extreme of wizards viewing mundanes as lower orders, wizards might enslave or otherwise control mundanes. In this case, they would likely avoid what they consider "property damage". This sort of reprehensible value is best suited for stories where it is thematically relevant; even then, be especially careful with this one, given the potential subtextual interpretations.
Other Concerns
Wizards have their own affairs. Possibly due to other factors (see Opposing Powers below), some reactions (including murder) might lead to distractions from a wizard's normal affairs, so they avoid them.
Leaders
Where "Mundanes Assemble" concerns an individual versus a group, this factor concerns two individuals: a wizard versus a leader. The power of magic can be balanced by the power of command by leveraging the potential power of the group.
Exceptional Circumstances
While, in general, a wizard is capable of easily killing a mundane, there might be circumstance preventing this. Something might have happened in the story that creates these circumstances, the most obvious being loss of power (so obvious, it could be cliche). This sort thing isn't so much a stabilizing factor (unless wizards commonly lose their powers for periods) or way of preventing magical murder generally as it is a situation in which a mundane accosting a wizard might arise.
Perhaps the wizard is trying to create or preserve a relationship, and flying off the handle would endanger this. Going the other way, a wizard might be making use of magic (no matter the consequences) in order to impress someone.
World Specific
Magical Limitations
Just because magic offers vast power doesn't mean it's also unlimited. It sounds like the magic system in the original question might not have many limitations. This can lead to an uninteresting story. Revising this to create direct limitations on magic can result in a more compelling story. See Sanderson's second law for more.
Scope
From the description, magic can create basic physical effects (possibly others). It's hard to stop physical effects from being used for murder for the obvious reason: deadly physical effects happen regardless of intent or even agency (fire burns, cold freezes, blunt force causes physical trauma &c) unless there's something that specifically counter-acts the magic, thus preventing the effect. The question specifically wants to avoid meta-magic and counter-magic for commoners (anti-magic fields may exist, but are expensive/rare), which only leaves room at the ends: what lets the wizard cast magic, and what happens after the spell.
At one end, requirements might not be met making the use of a spell impossible or there might be interference preventing the casting. Things like conservation laws and other physical laws (if present) might impose requirements for the spell. Energy to heat something has to come from somewhere, or go somewhere to cool it. Electricity requires a difference in potential and follows the path of least resistance; if you can't get the configuration right, lightning might not hit the intended target, especially if there's a nearby electrical ground (if lightning magic is common, settlements might have lightning rods all over them). It might not be possible to teleport an object into solid matter simply because two different objects cannot occupy the same space at the same time (though this wouldn't rule out transposing a chunk of someone's body with, say, a rock, air or their fancy new shoes they wouldn't shut up about the entire coach ride). The question mentions casting spell with a thought, which might be too powerful to be interesting. If a spell instead requires saying something or making gestures or using an object, a mundane might be quick enough to interrupt the casting. Spells might have what is essentially costly or rare ammunition, so wizards won't waste them on an annoyance. Even if only thoughts are required, it's hard to think when you're beaten about the head and adrenaline kicks in. If the thought takes time, this leaves wizards vulnerable (to slapstick humor, if nothing else). While there are many ways to limit the scope of magic, the real trick is to find one that's interesting. The story themes can inspire limitations that mean something.
You could go the other direction, making it possible to resurrect the dead, but that introduces its own narrative problems by trivializing death.
Fatal Flaws
It might be that wizards are glass cannons: while their power can't be stopped, they can be killed without too much difficulty, given the right circumstances. It might take an arrow-storm. Perhaps a magical trap; contract another wizard to create a cursed item that appears as something the wizard would want (a rare tome, a powerful artifact), and somehow bring it to their attention. It might be as simple as sneaking up on them while they sleep. Your average Joe won't be able to protect themselves, but they sure can retaliate.
If a substantial part of a wizard's power comes from outside them, this source might be more vulnerable than the wizard. The wizard will try to protect it, which can be the source of tension in the story.
Supernatural Consequences
Consequences are an indirect limitation.
If magic is tied to character in the same way action is (i.e. what type of person someone is impacts their actions, and vice versa), an act of killing will also have supernatural consequences.
Magical
Killing someone (either magically or mundanely) might create a magical stain that impacts their ability to perform certain types of magic. This is easiest to explain with theurgical magic, where a wizard invokes another entity to perform a task. This other entity might be able to detect a killer and refuse to work with them. Similarly, a wizard might invoke an entity, rather than communicating with them directly, to trigger the magic, and this entity might not like it if a wizard kills in their name too often. This can create a destabilizing factor, if there are also entities that prefer to work with killers, though this only provides incentive to wizards who want to work with these entities (and will likely be considered the evil wizards of the world).
Even if magic isn't based on invocation, killing might affect a wizard's relation to the source of magic. It might not even have a direct effect, but build up over time and the behavior of all wizards. Killing and other evil acts might poison the well, eventually harming the wizards themselves. The source might be sentient, semi-sentient or otherwise have a moral code or an incarnation that will step in and deal with wizards (individually, or en masse) that misbehave, or there might be feedback from the type of magic that gets used back to the source, changing its nature.
Spiritual
Killing could attract unwanted attention from supernatural entities. Killing might affect a later life (if there's reincarnation) or an afterlife. You could even try to work in consequences that supernaturally happen before a murder, though this is hard to do sensically. Of course, this affects all murder, not only magical.
Opposing Powers
Even if average Joe doesn't have the power to oppose the wizard, other powers might exist in the world. They may be on par with the wizards, or the wizards' power might not be as effective against them.
The Foe
Wizards might be engaged in a struggle against some other, non-human power. This both constitutes an Other Concern and can be a stabilizing factor in its own right. If the opposing power is a threat to mundanes as well as wizards, the mundanes will treat wizards with respect. Society might even be structured so as to support the wizards in their struggle.
The Foe might somehow benefit from people killed by wizards. An untimely death might become a soldier in undead army, or provide some sort of death-energy (such as souls-as-fuel), or affect the worldly balance of life and death. Perhaps it's simply a matter of PR, as the people's fear will lead them to align with the foe; the people don't even need to be aware that the foe exists.
A Foe is a major world component, and so may not be suitable if you want to focus on something else for the story.
Wizard Police
For many reasons, wizards may not want other wizards to act out their whims (such as wizard-on-wizard crime). Wizard society may thus create its own police force. This is particularly common in worlds where magic is secret.
Wizard Assassins
If there's money to be made, someone will take the job. A troublesome wizard will motivate the populace to hire anyone who has the power to take down the wizard, even if individuals can't afford it (see Mundanes Assemble above). This might lead to a class of wizards that specialize in anti-wizard combat. This will prevent many wizards from creating wanton destruction, lest the town band together and hire one of these assassins. Cheesy, if done carelessly.
Magically Immune
Some entities or people might be immune to some or all magical effects. These could form the basis of organizations to police wizards.
Wizard Society
While Wizard Police are a specific, hard power against misbehavior, wizard society (if the world has it) at large may have norms against killing mundanes. Even if wizards aren't concerned with exclusion from mundane society, they likely won't want to alienate their peers. Additionally, wizards raised or educated in a wizard society will largely take on the values of that society, which likely includes precepts against killing in various circumstances.
Secrecy
Some of the previous factors suggest situations where wizards must keep their powers hidden. This will not only rule out many magical murder methods for being too flashy, but may even any method that has a hint of magic, as it will put communities on guard. It could be used as a destabilizing factor; a wizard might surreptitiously cast a few spells (or a mundane might fake their effects) to amp up paranoia in a community and watch it tear itself apart.
Conclusion
The above categories and examples aren't exhaustive, but should cover enough ground to keep you busy.
Preventing magical murder happens in larger context, both diagetic and non-. There are likely other aspects of magic, such as limitations, that might end up impacting this question as side effects. Even the most basic magical spells, such as mending or light, would in actuality have tremendous economic (and thus social) effects. See "Magic rules without logical loopholes".
