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Why is defederation an option when Limit/Mute exist?
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Your problem is that you're still seeing the platform as 'controlled by users', which isn't how top down moderation works, the sites/instances are controlled by the ones who own them, they are the ones who call the shots and it is their job to enforce the rules and their choice to choose to kick someone or a site out of their circle.
A user does not have a say in this anymore than they have a say in other moderative decisions on the site. If a user's desire to interact with the other instance goes against their home instance's desire they have the option of migrating elsewhere or start their own. The fediverse is about having options of different platforms that can communicate with other platforms, not catering to free speech and user choice demands. The whole thing is still up to the individual sites and the people that run them, and they are not obligated to do anything for users (many will gladly put you in your place if you try) who they are graciously allowing to use their service.