You bring up a good point. What I had in mind is to pick one of problematic wars (meaning pick the one that looks very complex with many sides participating) and put a protagonist there. But the catch is that entire story is on the side that fights against US and NATO (these two go together it seems), but the protagonist is not doing actual fighting since he/she is a civilian. Now what I see as problematic is that propaganda bit, all games out there are very much 'US is a good guy' which is not really true if you use your brain, and is a form of propaganda against the nation that might play the game (remember: not trying to start a flame war here).
Since you would play as civilian that is on the 'enemy' side you would probably see much of the dialog that could be interpreted as anti-us/nato propaganda but it is only natural to root for your own side in every situation at least in some way. The war part in question would be either in progress or recently ended while protagonist goes around doing his thing. What I see as a big immovable obstacle with this is that no matter how the game and its story is executed if it could be shamed as anti-us propaganda game it can't sell anywhere. Stuff could be made even worse with internet/media backlash to such game.