I'd argue that the purpose of the state is to prevent people from doing certain things. To illustrate, most of our laws are "Thou shall not..." versus "Thou must..." to punish "bad" behavior instead of compel "good" behavior.
I'm wondering what basis you have for drawing the line there.
Personal autonomy. Your body, your choice.
Or why a simple waiver process wouldn't be sufficient to handle those who object.
Because a waiver process implies that it's the government's choice and not the individual's.
In general, I would argue that a state has the authority to compel someone into doing anything that has been sufficiently demonstrated to be a good decision
Can the state compel everyone to be a vegan unless they can show proof of a medical condition that would make it unworkable?