The game attempts to provide a moral dilemma, if you act in the way we perceive to be "good" then you're likely to loose something - but at the same time they hope you care deep enough about the potential consequences within the game to act based on emotions, rather than logic. It's not a great way to do this sort of thing, simply because, like you say, it becomes a repeated pattern that damages the players perceptions of "good" by taking away gameplay benefits.
One game I felt did the system justice was The Witcher, choices had consequences, yet there didn't always appear, at first glance, to be a "right" choice.