There’s an interesting post on designing games with moral choice (and moral ambiguity) over at Gamasutra, which looks at the Bioshock games especially and speculates about the value of moving away from super-simplistic black-and-white good and evil, which is a pet peeve of mine as well.
Something the article doesn’t touch on much, though, is why we are including these moral choices in the first place – something I think we need to know in order to decide what sorts of structure and context should be provided. Are we making a rhetorical point about something we believe? Are we telling the story of how a particular character in a particular context wrestled with moral decision-making? Are we pushing the player to explore his beliefs about a difficult situation (a la The Baron or Fate)?