I think that the way to deal with one's instance defederating from an instance who's content you value is to move to another instance. Admittedly some tool to move one's subscriptions to a new account would be helpful with this, but ultimately, this sort of thing is part of the point of a federated network, instances should be ideally small enough that one can be at least somewhat familiar with the admins, and so can leave if they don't fit you.

I don't think defederating an instance that one's instance as a whole finds distasteful is a bad thing though. Maybe if it was a decision that was very unpopular with one's userbase or something it could be a problem, but in general, it seems preferable to having to just put up with people you'd rather not be around/talk to, while still letting them have their space to themselves. People have the right to talk to eachother. But they are not entitled to talk to you specifically, when you do not wish to listen to them