@Polychrome I don't know much about how federation works, so I can't give a good answer, but my first thought is that there'll just be a pact/list maintained of instances that don't or do federate with FB, and connections will be based on that. You are correct, this will split the fediverse in twain, and I'm sure that concept has more headaches than I imagine.
But I have some amount of faith in the tech savvy of the people that develop this place. Some will have an easier time than others. And with any luck, FB will ditch within a year.