The nature of the fediverse is that it's federative/defederative. If an instance chooses to defederate because it thinks federation is a risk then they can do that. If that causes a problem for a user, the user can move to another instance which does federate.

I joined the fediverse after years of bad experiences on more typical social media sites, and specifically lemmy.blahaj.zone instance because the admins are very good at weeding out transphobia. If they federated with Threads I would be very surprised and want them to convince me of why that was a good idea.