I think the problem is lack of a clear data element that captures what you need. The current vote up/vote down system blends a lot of factors together, which is valuable for some calculations, but not the one you're looking for here.

I suggest a "flame" flag for every comment, which can roll up into a user's rating as a "flamer." The flag would only be available to HNers with a low flame rating themselves and a significant history of comments.

By default, no one would see comments that have high flame ratings. Users that accumulated flame points would get a time out from commenting, leading to a permanent ban if the behavior doesn't stop.

The site is wonderfully minimal at the moment, but using a UI graphic such as a fireball or flame could draw attention to the importance of civility.