Why do these communities need long-term persistence? You could use a separate archive based on plain web server mirrors for anything worth preserving. Maybe it's good that communities disappear and coalesce elsewhere, maybe it's evolution. Maybe being forced to pick and choose what to archive and what to let go is a good thing.
AP is a very chatty protocol and to handle large world-scale groups requires additions like compressed digest distribution, mirrors and sharding. Threads are already fragmented by design so in the end it may be unworkable to follow large group threads.
Some communities have to go through this cycle of banning everyone then realizing they're alone, then taking stock. If they're fine with this, it's a perfect result: they're niche communities. If they're NOT fine with this, their modus operandi is contradictory: they rely on recruitment but gatekeep too much. They'll never realize this until they go through the cycle. Let them.
As for not being able to separate people from their ideology, good luck with that and enjoy the cats.