They are long, but not uncivilized. That's the point - HN goes to significant effort to avoid long threads, and in my view a lot of our best information is contained in long threads.
If lack of civility is what we want to avoid, maybe we should target that directly.
The post I originally responded to was discussing various ways HN discourages long threads, at least relative to reddit. HN also explicitly penalizes stories with comments >> upvotes, and makes it difficult to reply to longer discussions via exponential backoff procedures (I know you can work around it by clicking the "link").
The reply-timer is not aimed at long discussions per-se, but to avoid quick-fire, heated back-and-forths between parties. The idea is that such exchanges are correlated with noise.
It's not relevant what it's intended to do, but what it does. If it makes long conversations hard, that's a con. (OTOH, if it avoids heated exchange, that's a pro. I don't really have a strong position one way or the other.)
If lack of civility is what we want to avoid, maybe we should target that directly.