Valkyrie Profile: Covenant of the Plume. Wylfred's father is taken by the Valkyrie, and he views this entire system of using human suffering to create and select the best possible heroes for the gods' own purposes as abhorrent and evil. However, when he gets an offer that's too good to be true- a magical feather that can eventually allow him to destroy the Valkyrie- he jumps on it all too eagerly, learning too late that it requires him to sacrifice a comrade, murdering them to further his vengeance. What's more, the story can go multiple ways, with him slaughtering everyone to turn himself into a monster of the battlefield, him trying to fulfill his role but losing his nerve, or even being completely unable to go any further with the monstrous plan after the first, arguably accidental death occurs.
I really like the story because no matter what decisions you make, there really are no 'good guys.' There are different political factions all wishing to stab each other in the gut to further their wills, and of course the gods, who are indifferent to humanity's own foolishness and depravity. It's easy to see how Wyl is easily able to further the plan in a world where the severity of murder depends only on whose team you're on, and there's always plenty of victims. And just as Wyl is blind to how terrible the power he's invoking is, those who ally themselves with him turn their heads at his obvious monstrous power, not caring how he does it as long as it furthers their goals. Everyone's so very ardently human in it.
But if that's too far from what you were thinking, I have another example that may be better:
Megaman X. Much is made of X's sacrifices to destroy his robotic brethren in order to protect Humanity from them when they go Maverick, but on closer inspection, this almost runs counter to the entire idea of the series. Megaman was about robots that had predestined personalities, but ultimately couldn't think for themselves. Reploids were supposed to be able to do what they chose. But every time that a reploid chooses to do something that humans feel uncomfortable with, tensions escalate and inevitably the Maverick Hunters get called in to squash the threat. This has the unfortunate effect of creating two different and stark 'sides' in the conflict, but also insulates humans from having to make difficult decisions about how to coexist with beings very similar but also very different from them. Ultimately the way the series progressed seemed only logical to me, as X keeps providing a band-aid so that humans never have to give up anything. I guess it depends on how you interpret "going Maverick," but for me it didn't seem as clear cut as the "murder program" shorthand that it was used as; I always sort of saw it as genuinely being able to do what they wanted, thus causing all the tension, conflict and war. I couldn't help but think that if the reploids had their own space, they would eventually have decided of their own accord that listening to self-aggrandizing leaders wasn't in their interest and had a better coexistence. But thanks to X always siding with humans, that never has the opportunity to happen.
