I wish there had been more examples of 'darkness' or 'poignant' games, or moments in games.
Personally, the No Russian mission hit home to me very hard. I kept myself in the dark about the controversy, allowing myself to bare the full brunt of what was occurring. Although there is no true reason to participate, i feel that not doing so would be against the message that the game is trying to put forward - do you simply sit back and watch slaughter commence, feeling the fact that you are powerless to do anything about it - or do you participate, sacrificing a part of yourself as well as countless innocent lives for the sake of peace?
More interesting would be if, halfway through the slaughter, the terrorists asked you why you are not firing on the civilians, perhaps questioning your loyalty. Do you then start firing, your choice now taken away with the threat of death on yourself? And even then, would your cover be blown anyways? Alas, that is not given to you, because that takes away the edge of the situation - if you have no choice then the choice has no meaning other then a means to an end. Anybody will kill someone else in order to save themselves (at least a person of weak will, like most people on the internet).
On a side note, a very powerful scene i found was in Far Cry 2. Nevermind the fact that your avatar has superhuman will (ripping pieces of shrapnel out of a leg, pulling a bullet out of a forearm with a multi-tool), but imagine the scene - you've just helped a comrade blow up a convoy full of guns for the opposing faction. You wipe the sweat from your brow, work the bolt to your rusty AK-47 to clear a jam, and stand out of cover - to hear the cries of help from your comrade.
You rush to his aid, finding him lying bleeding amongst scores of dead enemies. He has been fatally wounded - but an injection of your trusty morphine will fix him right up.
However...it doesnt. His pain remains constant, and he asks for another. Then another. Then another...before finally succumbing to the massive overdose of painkillers and drifting into a coma, to which he will never awaken.
...Alternately, you could give him a warrior's end, and put a bullet in his head, looking away as you do to avoid the grisly sight. He even grasps the gun barrel, making sure it is firmly placed on his forehead as you pull the trigger.
Of course, there is very little the game does to adhere the comrades to you, but as an avid 'sucker' (a person who gets sucked into a game and starts role-playing after a while - i personally liked playing as the old seen-it-all-but-doesnt-know-anything-different ex-military russian man), this choice could be quite painful. The choice between a bullet or a pain-free eternal sleep was sometimes hard - seeing as everyone wants to kill you, i didnt know when i would need my panacea in a needle.
Could i risk giving my comrade two or three shots, leaving me with barely any or even none at all? Even then, perhaps forcing me to put a bullet in his brain anyways, which leaves a bitter aftertaste to something that will already leave you with something that you'd rather not have.