Bodily autonomy doesn't apply when the choices made can affect many more people than yourself. I also don't think the isolation excuse works, as diseases can have carriers giving them a route to those pockets that aren't protected. Pretty sure we've seen that kind of flareup before, with the antivac crowds confused as to what happened.
Kids with medical reasons why they can't get a vaccine aren't a risk to the vaccinated group, they are AT risk, but they are much more protected within that group than with a bunch of unvaccinated ones.