When you went on a killing spree against civilians in GTA, or even Elder Scrolls, that was you. You did it, you weren't asked or expected to, it was just an option that you took (and the games would suck if civilians couldn't die).
In MW2, you are told and expected to carry out a terrorist attack on a bunch of civilians (for spurious reasons). You don't have to, although you are expected and told to, as part of your 'duty'.
Beyond that, it's a terrorism simulation. That's a much scarier and more offensive proposition than what's in GTA for your average American (or Russian as it turns out).
Personally it doesn't matter to me. It's a bit tasteless, but I'm not the kind of person to censor things I find tasteless, ultimately it's not that big a deal and it's not going to get kids into terrorism...
A game I'm developing with some friends:
www.xnagg.com/zombieasteroids/publish.htm
It is largely a technical exercise but feedback is appreciated.