That's the thing. Us already did this. In the first episode it claims the Joining was done prematurely once human authorities became aware of its existence. Resulting in the death of 900M people. Its handwaved over but this would imply that they forcibly brought the remaining humans onboard once that happened.
So now you have the situation where Us knows that the immune humans cannot truly threaten it, or something, but Carol can damage it's collective function on her own. Even if it is temporary. There needs to be a good reason why Us is so invested in the happiness of the immune rather than just corralling them into reservations where they cannot interfere with it and whatever its doing.