Sorry for the thread revival, but Alignment kind of came into play in my SWN campaign that just ended. The initial 'hook' for the players was that they were all meeting at the funeral of their friend who died under mysterious circumstances. One of the players was a priest who managed to convince his order to leave the monastery to pay respects to his friend. But low and behold (
) they get wrapped up in an adventure as they try to figure out the real murderer. Cue them scheming with the underworld, battling security forces, typical adventurer stuff.
Well, our priest's order found out about his illicit habits (though the player did well in role-playing his conflicted feelings to things like breaking into government facilities) and sent a 'team' to go bring him in, since they figured he's gone rogue. Cue everyone's surprise when an armed and armored hit squad of warrior-priests show up demanding them to hand over their buddy. Hilarity ensues.
Like Cyborg says, I play alignment out through consequences to the players. Since the game is sandbox, I rely on the back-and-forth between the player's actions and 'my' reactions ('me' being the government, society, etc.).