Perhaps we could have a mix: top level comments have karma shown, but child comments do not. This way when quickly scanning for a good top level comment to read you have something to guide you, but for nested discussions karma is hidden to prevent contention.
I'm not sure how much I like this idea, but instead of just arbitrarily cutting things off at top level comments, maybe comment scores could be shown as long as their parent's score is shown and they have more points than their parent.
The idea would be to highlight any path through the comment tree where comments are strictly increasingly valuable. So, for example if someone asks a question and gets a really good answer, the scores on both comments will be shown. The score could even be shown on an even better reply to the answer. But if someone trolls the really good answer, neither the score of the troll or that of responses to it would be shown.
A further improvement on this might be to use a time weighted value (where newer comments have more weight) similar to that already used in comment sorting so that comments have a chance to gain value instead of being pitted directly against an already popular comment.