The problem with that is, if they join, they will have the most active communities. Everyone will naturally want to use those instead of the less active ones in other communities.
So, in that case, defederation may end up harming the userbase. After that, they'd basically have to rebuild the communities that got abandoned for the larger ones on Threads. Some users may even jump ship to Threads to continue using the communities they've become accustomed to.
So the question is: defederate and potentially harm your instance, possibly even irreparably, or stay federated and continue allowing Facebook to do what it wants?
Not OP, but some corporations are "less evil" than others, or at the very least less obvious about being evil. "Evil corporation" means they're extra evil.