Yes, well.
What I got from the scene is not so much that it is a breakthrough in videogame narrative (it's not) or necessarily elevating games to 'art' (whatever that means nowadays and no, it's not). Conflicting opinions will be just that, and between media watchdogs and self-serving politicians, you've got a pretty cozy controversy.
I liked the scene for a couple of reasons. First, it moves players into uncomfortable territory. FPSes are no strangers to death and violence, and you can certainly argue that dropping a nuke and 'killing' a mute protagonist in CoD4 wasn't all that important given how you can spend the rest of the game 'dying' and reloading in a Looney Tunes cycle. But for the newborn perspective of this newer generation of players - console players, perhaps, but not all of them - it's a somewhat radical position. Traditional, by the rules FPSes are meant to glorify, to emasculate. Women are commodities and prizes. Headshots are the ultimate expression of manhood (and there's certainly something to be said of how it can translate into sexual pulsion, headshot as cumshot, the "other" subdued by our power).
But 'killing' the main character, that link that players establish with the avatar as a representation of themselves, is not as commonplace. Prior to this, you had what - CoD4's grueling moment of crawling outside the chopper and dying? Quake 4's amputation of the main character until he became the "other", the very thing he was meant to kill?
Yes, it can come off as cheap or not particularly "well done" - I suppose there are better ways to integrate that kind of 'message' into gameplay - but it's a step forward. In a genre where you're mostly killing everything and everyone is dropping around like flies as you are the hero, challenging your comfort zone is important. In this case, switching "hostiles" or "terrorists" for clear innocents.
What pissed me off, however, was
a) the German butthurt, which is entirely asinine as far as control of violent content goes considering how they have no problem giving freedom of speech to hate groups, which are responsible for more violence and brainwashing of younger kids than videogames;
b) the general "political correct" butthurt, which is sustained on the idea that "guys this is an important part of our game but you can skip it", which completely undermines the point of it;
c) the fact that the on-rails narrative is somewhat deceiving. The first time through the level one can assume that, given your threshold for what's on the screen - namely, if you can stomach gunning down civilians while a baby cries in the background - your first instinct might be to not open fire on them. When the level ends, Makarov shoots you point blank.
Now, on a replay, you might think that, since the objective is to go undercover a terrorist cell to nail Makarov, that you'd have to comply with the atrocity so that your cover wouldn't be blown. You start gunning down the civilians in the hope you've done a "good job" convincing Makarov of your allegiance.
He still shoots you.
Screw that.
Having him not kill you if you acted out your role, it would have made a much better point of driving the "in war sacrifices must be made" point.