but that when introduced to the thread has the effect of making it harder to discuss the article on its own terms

That isn't neccesarily a bad thing. I'm personally fine with a comment thread debating things unrelated to the article itself, as quite often articles aren't half as interesting and valuable as things that appear in the discussion thread.

and how unlikely it is that anyone will learn anything from the ensuing debate

I'm not so sure. Yes, some debates are being rehashed, but I'm pretty sure that barring few HN-ers who like a particular topic and chime in every time, we see the same arguments being brought up by new people. I suspect that at each iteration some people learn what they were supposed to learn and leave the conversation.