One doesn't have to take extreme positions to be consistent. In order to believe that someone should have bodily autonomy over continuing a pregnancy (something potentially life threatening, and definitely life altering) I don't have to believe that bodily autonomy is absolute.
Vaccines are something that touch on community health. When one person chooses not to get vaccinated they are putting everyone around them at risk. At the most extreme extent, abortion affects the potential parents, the potential life, and their families. It's a different risk calculation. A woman pursuing an abortion is making life and death decisions for (at most - because not everyone believes the fetus is a life with rights) two people. Someone not getting a vaccine in a deadly pandemic is making decisions that impact life and death for their whole community.