But it doesn't just penalize flamewars, it penalizes all conversations. For example, I have now posted two comments in this discussion and only upvoted the article once. Does that mean this is a worse article than one that I only upvoted and never commented on or a better article than one I upvoted and commented on three times?
Keep in mind that HN also has a "deep thread" mechanism, which hides the reply button for a while on sufficiently deep comment threads to discourage rapid-fire posting without thought. (Slashdot used to have the same thing; if you posted comments too rapidly, you'd get a "whoa, slow down there".)
I'd also hope that more weight goes to "more commenters than upvotes" rather than "more comments than upvotes", though as vague heuristics neither seems too far off.