It's been touched on before, but there's still more thought to be put into it: morality in MMOs, if you think about it, can be a touchy business at best. Scott Jennings recently took the opportunity to discuss the genre's stance in light of the Modern Warfare 2 controversy, pointing out that the genre as a whole has generally failed to touch on morality tacitly but has frequently done so passively. The game we play are almost relentlessly imperialistic, as he puts it, with an unambiguous march toward taking everything at gunpoint (or sword-point, or laser-cannon-point) and becoming the undisputed master of all you survey.
It's equally true in EVE Online, where the game implicitly sends you up against all other players in a bid for maximum possible gain, or in World of Warcraft, where you can find yourself invading homes for no reason or killing people for holding a legitimate grudge. The only games that even start escaping from the whitewashed attitude are superhero games such as City of Heroes and Champions Online, and even there you most likely send several thugs to the hospital without so much as an effort to negotiate. Whether this can or should change isn't easy to say -- much of the rationale behind it is tied to the game design rather than player choice. It's a topic worth considering, however, and one that will doubtlessly be addressed more as the industry grows in maturity.