That's a really good point. I thought that maybe you could solve this by dividing the story karma by the comment karma, but then you get the opposite effect; it hurts you to make a new comment on a front-page item and helps you to make one on a less-upvoted item. Maybe that itself would be a good thing.

Another approach would be to normalize the comment's score against the other comments on that story, and use a threshold on that. If there were 4 comments with karmas 1 to 4 and another story with 100 comments from 1 to 100, the 4 on the first would be just as good as the 100 on the second. That might be too much work, though ;)