Exactly! Since Vice City we've been playing as loyal characters. Since then it's been all about where the side characters take the main character, when it should be about where the main character takes the player.
Claude had no problem betraying Kenji in GTA III. Imagine something like that, in a far more emotional situation that has come with advancements in video game technology, etc.
Get rid of the moralist overtones and you'll be so much more likely to craft an amazing story. Not all characters need to do things that the audience agrees with and would do themselves in that situation.