It seems to me that many of the 'bad' comments come from users who has a strong feeling on a subject and therefor posts many comments on story, where one might get upvoted early on. I think it could be a good idea to account for the consistency of scores on comments by a user within a story.

Edit: I also think that the effect of the first downvote on a new comment is (or was) to powerful. Especially when the leading comments have many replies.