Very interesting point about not discouraging high value contributions: you don't want to create a situation where users have no desire (or are afraid to) comment.
> Most of the users that have a high karma count have so because they always have something insightful to say (mechanical_fish (http://news.ycombinator.com/user?id=mechanical_fish) is a good example), and their incentive for posting interesting stuff is marginalized by this. Almost all people, whethere they'll admit it or not, are incentivized by other peoples approval, eg. karma, and downplaying their contributions will make them more prone to not submitting great comments.
I think we can all agree that users with high karma generally have it for a reason. However, you can't always deduce that if user A has higher karma than user B, than user A has higher karma because his contributions are always more insightful than user B's. It's not a total order.
The marginal incentive ("get more karma by writing a comment that gather N+1 up votes") is not aligned with the over all goal of the sight (produce consistently insightful content).