An interesting subject Oolala.
It relates well to my recent experience playing Red Dead Redemption by Rockstar Studios. Its a great game by any account, but I found its pragmatic morality to be a little disturbing. The issue I came across was in the chapter of the game when you cross the border into Mexico in search of a former outlaw compatriot that in the past you had a falling out with for some undisclosed reason. Mexico at the time period in which the game is set, was mired in a civil war between the despotic government ruled by settler aristocracy and the downtrodden indigenous peasantry. The narrative is well written and the conflict is well fleshed out by the entertaining cutscenes. There was no ambiguity involved in knowing which side which you should sympathize with and which you should support.
The problem being is that part of the narrative is that the outlaw the player is supposed to track down and bring to justice maybe hiding with rebels and the main character which you play needs the assistance of government soldiers to track him down. The player has no choice but to follow the narrative and accept missions from government officials which involve killing rebels and destroying their homes, which are justifying purely by personal expedience. In order to pursue your personal goals you have to act contrary to your personal preference. Even when in other narrative branches you're actually helping the rebels and meet NPCs which encourage you to identify with the rebels plight and sympathize with them on a personal level. Due to the narrative, the player has absolutely no choice. This really grates on me and reduces my enjoyment of the game.
I don't know if anyone else has this problem playing.