Spoiler's ahoy!
Very interesting thread so far that has cleared up some of the confusion that I felt after completing the game - especially the player/game relationship[footnote]As in, you didn't have to continue the game and it essentially told you that you could have always quit instead of continuing Walker's murder spree[/footnote] is an interesting thing to take into account here; one that I hadn't so much formalized into a theory while trying to beat the game. And trying is the perfectly fitting description as the disgust of what you do while playing Walker steadily mounts[footnote]One of the most intense moments the game offered for me after the White Phosphorous scene was that helicopter attack on the broadcast tower - you can feel the insanity of what you are doing in that sequence and erase the last doubts that Walker is completely deluded by now[/footnote] until you finally gaze over the burning ruins of a once great city whose (second) demise you alone caused - a great downward spiral that the game (usually) knows how to employ and show.
However, as my personal interpretation I always saw that as more of a deconstruction of the hero stereotype and the modern shooter than a commentary on the nature between player action and the game itself. While it highlights that often enough and works in guilt-tripping you for what you do in the game and throughly questions the responsibility of the player it somehow seems a bit too inconsistent and those guilt attempts seem awfully constructed at times: as some poster above noted, many of those atrocities rely on miscommunication, that storm-wall thing is never properly explained[footnote]I haven't found 3 or 4 intel pieces in the starting zones so if there was something you can disregard that point[/footnote], the whole CIA thing and what the 33rd actually want to do is only hinted at for the most part and seems very constructed for lack of a better word[footnote]it's worth pointing out that the game probably wants to remain mysterious on the nature of those groups in an attempt to not provide any black and white painting of it's setting - possibly as a deliberate commentary on the nature of warfare. However, that somehow clashes with the expectation we have at the end - wouldn't it have worked much better if the 33rd was presented essentially as a bunch of monsters in the second half of the game, when Walker was thoroughly deluded already and then subvert that right at the very end?[/footnote] and, most importantly, the fucking "water supply" consisted of three trucks pumping water out of an almost empty swimming pool - considering the game mentions thousands of people in there how on earth could the city have "survived" more than a few weeks at most? The city was doomed to fall and as cruel and ironic as it sounds, Walker was probably the best chance of saving the inhabitants of this doomed city. His downfall is therefore a deconstruction of the idealistic hero stereotype in games, most notably of the MMS-genre.
As for the player/game relationship and the nature of choice, I think it's much less impactful than another game that managed to do this and was already mentioned in this thread: Bioshock. Bioshock went down the route of telling you what to do in pure FPS fashion and then goes on to say: "You thought you did that by choice! You didn't! Essentially like in every other game!!! Trololololol!!!". Free Will is an illusion in a video game and Bioshock highlighted this difference between freedom (Objectivist ideology, art-deco design, "sand-boxy-feel" of the game areas) and constraint (The city of rapture as a claustrophobic nightmare, the craving of the addicted as well as the player to adam) at every turn and, in my opinion, works much better in highlighting this dichotomy. Spec-Ops, however, seems much less out to do this than it is about flat-out telling you that what you are doing is bad by showing you the dire consequences that your/Walker's actions bring, bar any choice you might have had, coupled with moral dilemma's that are just too constructed at times. Hence I read it more as a commentary on the shallowness of most MMS games or hero-oriented fiction peppered with a strong "war is no game"-message than about choice, although especially the ending is a brilliant exercise in questioning the player's responsibility to his actions in-game.