I think it is important to make the distinction between player and protagonist agency, especially in games like Spec Ops. I never felt as if I was making the choice to fire the white phosphorous, but I rather considered it a decision on the part of the protagonist. Then I fired away with it gleefully (even though I did catch on once I saw the huge blob unarmed, unmoving people by the end of the bombing run) and accepted the resulting slow walk of guilt scene as something that was affecting the protagonist, not me as the player. Meanwhile, I also thought it had a second layer of "meaning" as a deconstruction of similar scenes in other military FPS-games where the resulting horror is rarely, if ever, shown and the whole use of WP/AC-130/Artillery/Whatever is meant to make the player go "wow, this is awesome".
To me it would seem as if most of the critique against Spec Ops in this thread stems from a confusion of player and protagonist agency. For this sort of game to work, one need to keep them very distinct and I honestly think that Spec Ops did make it clear that it was Walker's fault that the civilians got slaughtered, not the players. After all the main plot of the game is about Walker's descent into madness due to his own guilt, while the subtext is a deconstruction of modern FPS-games and their gung-ho approach to war. I think the game handles both quite well.