Well, in almost any video game, or PnP RPG for that matter, you easily rack up more kills than any real soldier or warrior likely did IRL in order to maintain a constant enviroment of action and challenge. The needs of an adventure game pretty much create a need for an unrealistic set of circumsances, which makes trying to judge things by conventional wisdom impossible, if occasionally amusing.
My basic arguement in situations like this is that it's justified due to all of these minions choosing to join the evil organization and follow the big bad, and/or by them trying to kill you. I mean technically your average soldier of the evil empire (whether it's a Nazi or a member of the Imperial military in Star Wars) could have chosen to not enlist, desert, etc... and take the penelties for that rather than deciding to tote a gun and try and use it on you. Given that the plot of these games also usually involves you doing something over the top, like say preventing the Nazis from summoning Cthulhu, it's even less morally ambigious since all of those guys between you and the big bad pretty much decided it was better to see the world flamed (probably due to promises of personal wealth and power) than try and stop the guys behind it themselves, or just plain out refuse to be part of something like this. In most games, though not all, your dealing with exceptional situations where any kind of real perspective is irrelevent. I mean even "historical" games trying to be realistic seem to give guys like Hitler an endless array of super-secret weapon programs hidden inside of mountain doom fortresses for you to go after and remove all moral ambigiouity from the situation.... the context of a game manages to make things both noble and a hero sane within their own own little virtual world, which is presenting a crazy situation to begin with. I mean it's hard to judge killing 1,000 people with a shotgun in a video game seriously to begin with given that killing that many people in personal combat is pretty much impossible to begin with, even for career soldiers in the middle of war. I suppose maybe you might be able to do it with artillery or cruise missles or whatever, but that wouldn't be the kind of personal combat we see in games.
As far as "Spec. Ops: The Line" goes, I never thought much of it's twist. But then again I've never been a big fan of deconstructionist movements when it comes to fantasy. You have to get into reconstuctionist movements for things to really get good to me. It's relatively easy to point out how silly the idea of a super hero is, or how F@cked up the events in a shooter video game are when viewed outside of their intended context, but when you can do that, acknowlege the points, and then rebuild it back into more or less what it was before, then your dealing with non-stop awesome.
To put things into a comics context, the deconstructionist movement was when people started trying to deal with super heroes in the real world (so to speak). Pointing out that costumes and masks were stupid, and asking the question as to why someone would rob banks or whatever when they could probably get people to pay them millions of dollars to use their powers in the private sector. The reconstructionist movement is when people started to point out that people still have conflicts, and those things are going to fuel confrontations, which in a world of super heroes means that those with powers are going to get involved. Wearing a mask is a way of avoiding accountability, since even as a good guy you don't want people to run around sueing you for saving their lives due to all the collateral damage if nothing else. People would rob banks because it's hard to finance a large scale agenda that people might not agree with if your earnings can easily be traced, etc... it all goes back to the same place it was to begin with, just with better explanations and more realistic motivations involved on all sides.
I think once people manage to concede some of the points made in "Spec Ops." but then manage to turn it back into say "Serious Sam" or "Duke Nukem" or other basic shooter while conceding it, it will be when the genere's writing has really come into it's own. The trick isn't so much to point out the absurdity of the number of people being killd like this strip and how the person doing it must be insane, but when you can acknowlege that, while still also conceding that the hero is sane and heroic despite everything he's done, with a full understanding of it.