Yes, this is a problem. I think the solution might be to have a 'vouch' style link on stories that get penalized this way, so users can say whether they really are flamewars or not. If they aren't, the penalty should come off. We do this manually today, but we don't always see the thread in time.

Of course that leaves the harder problem that some of those threads are flamewars rather than civil conversations, as the guidelines call for. But fortunately that's not always true.