Well one way could be to use the karma points for general gameplay (for example killing a little creature that is no threat and not doing anything wrong is bad for you karma). And not for the bigger (and more complex) moral dillema's. (=> so noone judges noone) Those dilemma's will just influence the story and your reputation towards the npc's involved. And as long as you don't overdo those dilemmas this should be easily possible.
But what exactly do you guys mean with "karma" ? Because I'm getting the feeling that what I think karma is, isn't the karma you think it is. (or something like that)
