That's a very interesting article, and one that has been repeated at infinitum and never seems to get into developers' heads.
Designers of these games have often lamented that so few people take the "bad" path, and much creative energy has been spent trying to find a perspective that encourages players to give in to the Dark Side or, more interestingly, to present choices that aren't as obviously good or evil.
Wait, what? Really? Are you sure of this? Really, really sure? Because every time I see a thread about which path people took on a game, about 90% of the people will say they chose the evil path. If they played once, they played evil. If they own the game, they played evil four times, did a good run to see what it was like, then did a genocidal run to offset it. As a matter of fact, I've come to see morality thingies on games as just a way for gamers to feel even better about being evil. Not only do you get to kick a puppy, a message even pops up saying 'Kicked a puppy! +50 Evil Points! Thrice Damned Bastard evil level reached!'
I remember the Prototype devs saying they didn't put a morality system in their game because they saw people playing and realized everyone just plays as the most evil bastard. I usually play as a good guy but even I felt that was a fresh perspective.
Susan Arendt, for instance, chose not to steal the cash from the couples' safe because she established her own personal context for the action.
Reminds me of the guy in one of the Escapist articles whose personal yardstick for evil was that he would not kill a goat in one of the King's Quest games. Or... can't remember who, it might have been one of the Escapist columnists, who said he loved foxes and so wouldn't hurt a fox in Red Dead Redemption... then hunted a fox to complete a sidequest and felt horrible about it.
The problem is that there will always be THAT GUY who would shout at Arendt saying 'WHAT THE FUCK IS WRONG WITH YOU, ARE YOU DAFT? THE ITEMS ARE THERE, THERE IS NO NEGATIVE CONSEQUENCE FOR PICKING THEM UP WHATSOEVER, YOU ARE STUPID FOR NOT TAKING THE FREE ITEMS YOU MORONIC IDIOT!' (Poor Susie!) The point is that some people will always focus on gaming the system, and will consider a stupid choice to not take the most advantadge possible even if it means your character is acting like a bastard. Of course, a game is about bending rules for one as much as it's about telling a story for others, although THAT GUY will usually say that his way of playing is superior and use his superior game stats as proof.
And, of course, while there's some obvious conflict in the way things happen in ME, I remember an atheist complaining about the morality system in Fallout 3, in which you lose karma for stealing stuff even if you aren't caught. He said it makes it look like there is some sort of force always keeping track of the player. Well, there is, but it should be a gaming abstraction, yes?
(And I've found a lot of hate for the bad end for the Tenpenny Tower quest, even though I personally think it's one of the only quests in the game to really mean something. Congratulations, you worked hard for the best end and now everyone is happy! Except the people you just helped are bigots and they kill each other. You know what they say about the road to hell and its pavement.)