Morale is exactly like any other part of customization you might offer the player but morale is bit stronger factor than let's say sex, height or hair color. Relating to a pink haired dwarf of different sex (as indicated by WoW) is easier than imagining themselves as an animal torturer.
The safe way to go is to avoid moral decisions made by character if you aren't going to offer the player any choice. Other than that it's a matter of choosing your target audience. As we know people play all kinds of games today ranging from being assassins to building their drug dealing empire to helping your neighbor and saving the human race from an intergalactic threat. Killing is everyday in games but so is completing task and quests for reward in mere experience points.
I think if you are going to go towards twisted morale it is important to make it sort of the point of the game and not just something that pops up in the middle of immersion. Make your intentions clear from the start and you'll reach the audience that are prepared and will enjoy stepping into villain's shoes.