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.
I think a big problem with a "harsh debate climate" is that the people who can provide real value with experience, knowledge and insight will stay away. For different reasons like personal, professional or just disinterest. That will in turn attract more people who enjoy a harsher debate, which most (if not all) of the time are less enlightened.
Or as the saying goes "Never argue with an idiot. They will drag you down to their level and beat you with experience."
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.