A couple of weeks ago here at PopMatters, Eric Swain wrote about a more complex form of moral choice in games.
It’s not a question of right or wrong, but a question of priorities. The player is offered up two rights and asked to make a choice between them ... The morality here isn’t based on abstract rules, but on the individual player—what they would do and why is up to them” (Eric Swain, “More Thoughts on a More Complex Form of Moral Choice in Video Games”, 24 June 2014)
I agree with everything Swain has written, but I’d also like to add an important caveat to the conversation. These kinds of complex moral choices, the kind that force us to choose between two philosophical truths that will go on to define who we are, what we value, and how the game is about what we value, these kinds of choices are best implemented at the end of a game.