

(Favorite Trope) "Necessary evil" villain genuinely doesn't like what they do and/or hate themselves for their actions. Bonus points if their actions are genuinely necessary
Edelgard (Fire Emblem: Three Houses): The world of Fire Emblem Three Houses is rife with inequality, with rapidly fading bloodlines being seen as superior to normal people even when you can clearly see just from gameplay that isn't true. Furthermore, it's being ruled by Rhea, someone that while not malicious is deeply traumatized and paranoid, incapable of ever truly understanding the human condition. While even after her death in most routes the world is changed for the better, none of those changes would've been able to happen if it wasn't for Edelgard's war exposing them. And between the main theme implied to be from her perspective, and her accepting her death with dignity in every route she dies in, it's clear she doesn't hold herself or her actions in high regard.
The Batter (OFF): This one isn't explicitly confirmed, but OFF is a very vague game because the creator Mortis Ghost intends for people to form their own interpretations, considering even his own statements to just be headcanons that can be ignored if you want. There are many things pointing to The Batter not wanting to purify the world. He implies that he's afraid of what he has to do, he might consider himself an "evil puppet led by a blind entity." He even implies that even once everyone else is already dead, even if he did kill The Judge, without The Player controlling him The Batter wouldn't be able to go through with flipping the switch to turn the world OFF.