It's important to note that the admins of beehaw are not happy about this solution, either. And they hope to refederate once they have better tools and enough mods / admins to deal with it.
They point wasn't to shadowban, that was a side effect. The point was to protect their member--who specifically wanted a certain type of safe friendly instance--from hostile weirdos sending dick pics and stuff like that. Nobody's happy with the situation, but it's the best they could do under the circumstances with the resources they have.
I also don't think it's wrong for instances to have their own strong rules and preferences. This is one of the GOOD things about the Fediverse. The software features and how people use lemmy will catch up eventually.
As for the confusion / chaos around multiple/redundant/competing communities and so on...that will get better over time as people figure things out. Honestly it's not that different than reddit with all of its splinter subs like "true-" whatever.