It's too early to know how exactly it'll be implemented, but I'd bet there would likely be a toggle/setting to turn on at the very least. I'm sure the upgrade instructions will be early laid out how to enable it.
You'd have to be significantly more careful with backups, as it's really easy to effectively "burn" a domain from federating over AP ever again (at least to instances that federated with it before), but otherwise it should be reasonably automatic as federation gets implemented piece by piece.
As someone who has very little experience with ActivityPub but is always interested in learning more, what's the risk of "burn"ing a domain? Does it come from certs or signatures changing on the same domain, causing it to no longer be accepted or something?
it's partly because everything has public/private certificates, but also partly because there isn't much synchronization going on after the initial "push". if you shut an instance down and modify the database directly without informing other instances (say, you remove an account) then other instances will not be able to tell and will drift out of date, essentially making that specific thing unusable for any instance that has previously interacted with it. if you expand that out to, say, wiping and re-creating an entire database, then you end up with so much uncertainty that you may as well start over from a fresh domain