Misskey is like mastodon so you can just go to another misskey instance.
But if you're talking about the misskey.io instance, it's not that defederated from my experience (the 3 instances I'm on aren't defederated from it).
The instance simply follows Japanese law so whatever Japan allows they allow and whatever Japan forbids they forbid (which is why censoring genitals is also mandatory in that instance lol). It's not like it's some nazi cesspool or anything like that.
Baraag is way more permissive than misskey.io and it gained a pretty bad reputation in the past because of that, plus it essentially advertises itself as a safe haven for lolicon art and primarily focuses on that, so that's why it's on many block lists.
misskey.io is just a generalist Japanese instance (which is why many Japanese artists easily hop on it). It's also the biggest misskey instance and is run by the main developer, so it's usually not blocked by default because most people use it.
Defederating from misskey.io would be like defederating from mastodon.social. Some will do it but it's not the default stance afaik.