Partial Fix #1:
We put together a special forum (subset of threads and posts) for a number of old argument topics, and make sure that it is readily accessible from the main page, or especially salient for new people. We have a norm there to (as much as possible) write out our points from scratch instead of using shorthand and links as we do in discussions between LW veterans.
Benefits:
It's much less of a status threat to be told that one's comment belongs in another thread than to have it dismissed as happened to adefmay.
Most of the trouble seems to happen when new people jump into a current thread and derail a conversation between LW veterans, who react brusquely as above. Separating the newest/most advanced conversations from the old objections should make everyone happier.
I find that the people who have been on LW for a few months have just the right kind of zeal for these newfound ideas that makes them eager and able to defend them against the newest people, who find them absurd. I think this would be a good thing for both groups of people, and I expect it to happen naturally should such a place be created.
So if we made some collection of "FAQ threads" and made a big, obvious, enticing link to them on either the front page or the account creation page (that is, we give them a list of counterintuitive things we believe or interesting questions we've tackled, in the hopes they head there first), we might avoid more of these unfortunate calamities in the future.
I'm not sure there needs to be more than one FAQ thread. But lets start by generating a list of frequently asked questions, coming up with answers with consensus support.
And happy new year to everyone.