Ah, sweet morality: the twisted and sickened sibling of utility.
The thing Mr. Butts (superb article, by the way) and most commentators seem to be chafing at is that it's possible to be a two-faced wretch in a video game without any consequences occurring. Hypocrisy is not only offered as a possible choice, in several instances, it's expected and required for progress.
Good people, let me enlighten you: That is how the world works.
Look at any politician and you'll will not see someone that can show a sparkling facade of virtue while at the same time cheating on his wife, plundering the wealth in his charge, and abusing the power he's been granted. Except when you do. Look at any religious authority and chances are you won't find someone who professes to want peace unto all while at the same time damning the unbeliever to an eternity in flame. Unless you do find that. These contradictions have manifested often enough that we have cliches and stereotypes aplenty for them: absolute power corrupting absolutely; people who talk out of both sides of their mouths; doing what you are told as opposed to mimicking what you see. And now that gaming has progressed to the point where morality is becoming an issue in role playing, you're complaining that it isn't complete enough or realistic enough to be relevant because every single solitary action you take doesn't have an appreciable equal and opposite reaction?
Folks, the games are doing a great job at showing us how things are and demonstrating that morality is not an easily measured quantity nor is it an absolute one. If I loot a corpse or decapitate someone and then search his corpse, the only real difference is that in one case I actively caused the situation and in the other, I reacted to it. Does my murder justify my theft? Does the fact that I did not murder justify the theft? The debate is still raging all across the world with a near infinite set of arguments yet here you are, expecting developers to hand you a ready-made solution instead of saying, "You're a grown up. You figure it out."
The reason this wasn't an issue years and years ago in gaming was because there was only one way to obtain resources and/or recognition: kill enemies. You make Grog slice open a lizard man, the body drops a fire mod for your attack. You slay the mighty dragon, the town is saved. You jump on the Goomba's head, you score one hundred points. Now we've progressed beyond that, to a place where scoring doesn't exist and you can use whatever you want to achieve your choice of possible goals ranging from the simplistic (find the macguffin) to the elaborate (take over the universe). You can modify anything about yourself and play any range of character with one stipulation: You are going to be judged on how true you are to your character. Most of the time. We'll let you know when. After the fact. When you can't do anything to change it.
Role playing indeed.