Star Trek has a few stories along this line. There is the The original series (TOS) story that was paralleling the Vietnam war with Kirk standing in for America and the Klingons were the Soviet Union and both were arming different sides in a civil war. This is especially useful in situations where the higher beings and the evil beings are powerful enough to wipe each other out in open conflict and was one of the ways the US and USSR could go to war with each other during the cold war without the nukes flying. Arm the guys who want to kill the guys the advasary is arming (not the enemy... in the US military at least, the true enemy is the Navy.). The "Prime Directive" episodes also dealt with Federation law which prohibited the heroes from with directly interfering with a species that had not yet developed Warp Drives (reasoning that the species that does would have to deal with aliens anyway, and offering species stuff they hadn't earned would pollute their own culture) OR taking a side in a developed nations internal politics. The Next Generation era (TNG, and includes Deep Space Nine (DS9) and Voyager (Voy)) were alot more strict about this rule than Kirk era was, which allowed conflicts with what happened if the primitive race was polluted. Look for a list of episodes that have this as a direct conflict (TNG's First Contact is a personal favorite and flips perspective of the "Alien Infiltrator" stories in fiction.).
Alternatively, higher beings do not have the resources to help the villagers... they are only there because evil is there and once evil leaves, they have no stake in the reconstruction. Since the logistics (supplies and shipping them) are often neglected in fiction, this would provide some realism and isn't a political parallel.
Alternatively, the higher beings are consumed by their will to fight the evil race that they are obsessed. Helping the villagers would slow down the defeat of evil... perhaps even allow them to regroup and strengthen. Whether the threat of that is real enough to justify this is perfectly fluid. Lack of a real threat means more obsession. Actual threat means that the highers do have a point.
A treaty between the evil and highers that puts directly helping the primitives in anyway beyond assisting in battle. Of course, like all good treaties, cheating will happen (don't believe me, look at the Washington Naval treaty, which governs classifications and limits Naval power among modern countries (it's post WWI, so it's old, but Naval warfare changes very little). Then look at all the fun ways the countries cheat. Most of it is illegal but Nation A won't call foul on Nation B because Nation A is just as guilty of creative interpretation. Alot of it is insestent terms i.e. the United States only operates 11 Aircraft Carriers. Those 20 other ships that launch and recover aircraft that just so happen to look like Aircraft Carriers the rest of the world uses? Those are Amphibious Assault ships, not Aircraft Carriers.). Can be further complicated if the Evil race is blatantly cheating but the higher race is moral enough to still play by the rules.
A neutral third party (NTP) that is just as, if not more, powerful than the highers and the evils decreed no helping the villagers. Said NTP should be a sleeping giant and either due to the ongoing war or just naturally so, they are more powerful than the Highers and Evils. As much as the two powers hate each other, NTP entering would be bad news so they comply.
The Villagers are non-particularly loyal to the Higher Beings... this would mirror recent American intervention in Syria which boiled down to a fight between a regime most voters did not carefor verses a rebellion group that was infiltrated by Al Quada (sp) by the time the US government decided to try and get involved. No one was thrilled with the prospect that arming rebels would result in arming an organization that wants to kill Americans as part of it's major mission statement. More historically, America was none to thrilled to enter both world wars because that was Europes Problem, not ours... even after Pearl Harbor, Americans were content to prosecte only the Pacific theater... it was Hitler declaring war on the United States that triggered the European Theater participation. Either way, the attitude boils down to "why are we sending our troops to die for their problems" as a popular political element in the Higher Powers.
Again, this also depends on which side in the conflict is your POV character. If this is about the Higher Power, than a "Prime Directive" is something you want to go with. The Highers treat it as near sacred doctrine and it's hyped as a sign of their enlightenment, but it's flawed in that it inheritly puts value on lesser beings.
If the Villagers are POV, you want to hype that the Highers are nice to have on your side, but are jerks.
All this said, I like the idea that this conflict has some politics to it. It's easy to say one is the purely pure good and one is the dastardly evil... it's a lot more complicated to say that the good guys and the bad guys are not black in white. One of my favorite series as a kid (animorphs) had this as a rule. The evil empire was governed by a democratic elected body and the head of the government's only true power was to cast tie breaking votes (if there was no tie, he didn't get to vote) and was never publicized for the dual purpose of security and power limitation purposes (it's hard to have a cult of personality for a leader when he or she is unnamed.). Meanwhile the good governmnet was controled by a xenophobic military command that at least twice enacted genocide policies to try and deprive the evil empire of resources and had a very censored media because they did not want their own people to find out about some of their war crimes (we learn pretty late that civvies in their society were much nicer people... but our heroes had the misfortune of dealing with the military more than the civvilians).