Double-dipping will most likely make you evil anyway over time. So some stuff will get automatically locked away if you try to double-dip. And even if you could manage to stay 'neutral', really good and bad stuff would stay locked away.
Questing for a evil one makes you infamous, killing him afterwards perhaps gives you bit good back, but will it compensate the bad influence from the quest? On the other hand helping someone with something good will give you fame, but killing him afterwards will be most likely worse. Evil acts have always bigger influence than acts of good.
I agree with just about all of this :P
Maybe you could try and flesh out the karma system idea? You seem to have a much better handle on it then I do and it seems what your saying might actually make everyone happy or at least need very little tweaking for all parties to be satisfied.
