Let's start with some basic neurophysiology (all that will follow is a simplification, but functionally correct).
There are three major areas of the brain that all work in different ways; there is the cerebellum (instinct and autonomic functions, hard-wired electrical), the limbic system (emotions, chemical) and the cerebral cortex (intellectual thought, soft-wired electrical).
Why three different systems in a single brain? The short answer is because evolution can't just shut down a species, redesign an upgrade to the brain, and restart that species. The species still has to function, so it develops a new system over the top that provides advantages over the old system.
Many animals, including insects, get by with a rudimentary cerebellum alone. It drives them to specific behaviour that increases their odds of survival, and keeps their systems functioning. (heart, muscles, et al)
The problem with that is that once you know the instinct, you can exploit it and create a set of circumstances in which the instinct works against the organism. Just take ultraviolet bug zappers for instance. Spiders (by the way) have been doing the same thing for much much longer, with webs that glow in ultraviolet, but I digress.
So, evolution builds an 'upgrade' for the brain that provides some situational overrides to instincts. It can't build it as an electrical system, that would mess up the instincts that work most of the time. So, it designs the limbic system, or reptilian brain. This is chemical in nature and allows organisms to feel emotions and react in specific ways according to environmental considerations. This is a great leap forward and allows certain animals to be more successful as their emotions can override their instincts at times to preserve the young, or push through pain to find food.
But, even that's not enough. So along comes the cerebral cortex, or mammalian brain, which not only allows for situational awareness, but actually allows us to 'program' our actions according to intellectual logic. This means that we can finally react and adapt to a changing environment within the lifetime of a single organism, rather than taking hundreds of thousands of years to do so. This makes mammals even more successful, and eventually leads to an organism that specialises in such thought - humans.
The point being, we don't know how alien brains would form. At all. What if the cerebellum in an alien species was based on programmed chemical transfer? The limbic system may not even exist and an alien may have evolved directly to a cerebral cortex model. What if the Earth's limbic system was more flexible and actually allowed for programmable emotions? The cerebral cortex probably wouldn't exist today as it would represent an added complexity that may not be required.
We break up 'thought' into concepts like instinct, emotion and reason because our brains are wired that way, but in an alien, not all of these concepts have to exist - indeed none of them may exist and their brains could have evolved along completely different lines again.
The important thing to note is that we have these 3 tiers within the brain today because our environment made this the simplest way to gain the complexity required to deliver the survive-ability outcomes that were required by humans to continue to exist and thrive. In a different environment, different stressors may apply, different 'starting' neurophysiology, different speeds at which organisms can change and still be successful. Evolution will never favour change faster than it is necessary in an organism, and never favour a change that is more complex than necessary (true, some systems seem needlessly complex, but like the brain that's largely because they're built over systems that supported previous environments; simpler systems that achieve the same end will always prevail over complex ones that aren't more effective because there's more that can go wrong).
To that end, it's entirely possible that aliens could end up with a completely different neurophysiology but by definition, that would result in a completely different psychology as well. One that may well be more pragmatic than our own.
For example, the cerebral cortex evolved after the limbic system, yet we still value our emotions despite the cerebral cortex evolving primarily to override it in certain situations. We fear and devalue sociopathy, but from certain perspectives, it makes the people who have it more 'successful'. I'm not saying that's a good thing, I'm merely pointing out that we are confused ourselves about the relative merits of our own thought chains. Aliens with a completely different brain design are just as likely to suffer from the same level of confusion, just against concepts of thought that we have no frame of reference to even begin to understand.