Preempting the flaw in your strawman doesn’t invalidate it. A woman choosing to abort a pregnancy has no bearing on anyone but her. In contrast, the anti-vaccine crowd both directly, and indirectly, contribute to the propagation of disease.
Your right to bodily autonomy stops at society’s doorstep, which is broadly agreeing that the unvaccinated don’t get to participate in the non-essential aspects of society, otherwise furthering the risk to everyone else without reason.