I think choice and consequence in games is very difficult to get right. I would prefer a system where a choices are a bit grey. I've never liked that I got bad points for not taking that injured werewolf guy with us in Fable. Hey, I was just trying to protect the group by taking no chances, sorry if that was cowardly .
Just decisions shouldn't always result in good consequences. If you carry out quests in a Ned Stark fashion I would hope sometimes you will have to feel the sting of that. For example if you hand in a criminal on the run, you should be attacked by his cronies and if you don't you should be paid off