Defederation with them will be a shot in the leg, and handicap the Fediverse movement itself. There will be users/instances in the current Fediverse that would want to federate with them, and banning such instances would create silos and echo chambers.
I don’t quite follow this line of thinking. Instance A can still be federated with Instance B even if Instance B is federated with Threads.
The greater danger, IMO, is the open source Fediverse losing users to Thread because of the slicker interface and greater engagement.