Lol, that's the one I came across.
It's interesting, but I don't agree. I feel there really is a difference: both in intent and in form (WHY you're killing, and WHAT you're killing).
In an open-world game, you go on a killing spree to chill out from the objectives. It's a way of taking a break. It's basically a minigame, like drinking alcohol (in W_D at least) or gambling. It isn't the intent.
Further, in games typically the antagonists are "bad" people doing something "bad" and thus you have a reason to kill them. Now, if you don't believe it's allowable to kill people doing bad things, this point probably won't mean as much (for someone like, for example, the author of that article). I DO believe it's allowable FOR CERTAIN THINGS. Obviously not theft. But if someone's in the process of, say, running a slave ring, and you are after the head honcho, I believe that if guards that get in your way, try to kill you, etc, it is morally...understandable, at the very least. I'm not a pacifist.
Incidentally, a game that did this on a large scale (if the people you came across, guards and such, didn't try to kill you but tried to arrest you), would be interesting from a moral standpoint. I'll never forget the ONE combat encounter in Dragon Age Origins where you come across a bunch of adventurers heading to Denerim to tell on a member of the Mage Collective, and they don't attack you--you have to choose to attack them. Those are two different moral actions.
But not only are these people trying to kill you and such, they also can be considered "bad people" in most cases, and are definitely not innocent civilians. So there's a large gulf, in my opinion, between the two. Not only are they inviting your response by assaulting you in the first place, they also are (typically) "bad" people who are "deserving" of some punishment.
The reality is, in most games what you're doing is passive. You aren't killing these characters, you're defending yourself from THEM trying to kill you. The person who chooses to kill and the person who kills out of self-defense are two different people.
I feel a story like this could do a better job of actually exploring the mind of killer (serial instead of mass murderer, but it's something) than a game that's just about mindless violence. Because killing is never really about mindless violence. There is intent behind it. And I admit that was a shameless plug, but read it it's good! Edit: It's not bad, but there are a couple of high points.