I get what you mean, Gaspard - and from a writer's point of view, if the player actually cannot bring themselves to play 'evil' because they find it too distressing/repellent, you know you're on the right track.
Equally, if the player's so disengaged from the world and the characters that their in-game persona can cheerfully run around murdering wholesale without them having any kind of thought or regret about their actions, then you've failed...
But in PARPG, we should be trying to cultivate a confusion over which side is which. How many times have you run into a goblinoid camp, killed everyone inside and then looted the bodies, before going home to your virtual wife and kids to smoke a pipe and warm your slippers by the fire?
You'd never do that with the "good" places, so we must make the distinction hazy to the point of non-existence.
You'll just end up picking one group of survivalist arseholes and hoping they don't get worse.