I think that the best thing to do with nuanced evil is to use it as a source of internal conflict for the players.

A lot of games overlook the notion of creating a conflict within the audience, but it's a perfect place to explore the concept because it's not just a question of "who exactly is this character, and can I relate to them?" like in passive media but goes a little deeper into "what do I do in this situation?"

One of the things that I find helpful is to frame the players' actions with an evil character as tangential to the character's evil. That is, they can help the character and do what is right in their faction/culture's point of view, or oppose them and get in trouble. Either way, they're not directly doing evil, though they may have some really hard questions to answer about why they acted the way they did.