This post over at Rock, Paper, Shotgun points out the trick StarCraft 2 pulls on players with the way it handles their decisions. I noticed it also, and thought it was interesting. But it isn’t hard to figure out this is what’s going on while you’re playing, especially if you compare your experience with that of a friend who made a different choice. And to me it sort of feels like it cheapens the story.
In a way you could say it takes the player’s choice away from them, in that the things the designers decided would be true (that Jim Raynor is right) are always true. It becomes obvious that the story has no meaning, that it’s just a rationalization of what’s going on, and at that point one may start to wonder why it’s even there between the gameplay at all.