If lots of instances start defederating them, then their users are going to start complaining to them that they don’t understand why they can talk to some people, but not other people.

I don’t think so. The most probable result is Meta (and maybe Google, Amazon, etc) running the mainstream instances, and sn alt-fediverse of smaller, tech-savy instances that defederate them. Most people will have only an account in the Meta-fediverse, and only a minority in the alt-fediverse or in both. Similar to most people now having a WhatsApp account, and only a few using Telegram or Signal.