I think a good idea would be to make it have 2 routes, 1- the standard roguelike experience where you kill stuff and get gold and keys, but here, given the context, would be the 'evil route' which should have kind of con for doing it, like shops not opening or monsters running away from you.
Then theres the the second route, 2- 'the pacifist route', where you know the "monsters" are people, so you avoid fighitng with them, or maybe you "pacify" them instead of killing them, like knocking them out of combat or something, to contrast the evil route the game should be harder but also should reward you for being a "pacifist", like "people" giving you free gold or gifts, etc...
What do you think?