Of course, all sides are wrong in somebody's eyes; so no matter what you do, you will be defederated from by at least somebody.
The way Mastodon works, defederation irreversibly breaks all follow relationships, without notifying those involved. If you disagree with the decision, you can migrate to another server, but you won't get your followers / followees back, not without everybody involved doing a lot of manual drudge work. This is just one way in which the myth of "users are free to do what they wish, if they disagree with the admins, they can migrate somewhere else" breaks.
To make matters worse, there's no way to see which users that you may wish to follow are / will be hidden from you if you choose a given instance. Defederation lists are a (somewhat open) secret; it's good practice to announce defederations, but there's no automated API endpoint to see them, so there's no way to answer the question of "who am I going to lose if I migrate from x to y."