Shouldn’t the same argument be used to persecute pro-choice advocates, women who get abortions and doctors who perform them?

This issue is much simpler if you rephrase it: replace the "pro life" label with "anti woman". As long as the child is connected to the body of the mother, we as a society decided it's more important to give mothers bodily agency than any rights of a potential human. Do not get tangled in the definition of when life begins, this issue is not biological, it's very strictly a decision the society needs to make. And while you think the decision is not clear cut, it actually is, you just need to look elsewhere where soceties made a decision on bodily agency: organ donors after death. I never heard of any place where it is mandatory to be an organ donor -- actually most places are opt in. So, apparently even your cadaver deserves bodily agency. If we consider the agency of a dead body can be more important than the life of several adult humans then how on earth can the agency of a living body be less important than someone who is not even born yet (might not survive etc)? Hypocrisy much?

Sure, and you could similarly replace "pro-vaxx" with "anti-freedom". Then it becomes a bit harder to stomach, no?

The point is, women are free to abort unborn children. They're not free to let their (born) children die (of neglect). It's not an obvious choice whether they should be free to not vaccinate their children or not.

> It's not an obvious choice whether they should be free to not vaccinate their children or not.

I mean, it really is. Not vaccinate can lead to death, not always but it massively increases the risk to the point that I consider it neglect. Just as a child left on the street may survive, it doesn't stop the path that put that child on the street being termed "neglect".

(I am pro-choice and pro-vaccine)

How can you be for bodily agency and also be in favor of forcing people to get vaccines?

Note first I disagree with allowing to opt out of your body used as an organ donor after your death.

No value is absolute. Trolley problem and all that (Judith Jarvis Thomson phrased the trolley problem as an organ transplant case it so happens). The potential destruction wrought by an unvaccinated child is deadly enough it overrides the individual bodily agency. By taking away the bodily agency of one child you are potentially saving several living, actual humans. When you take away the bodily agency of one woman, you are potentially saving the life of an unborn person at best. This doesn't compare favorably. Also, beyond bodily agency we need to weigh all effects of forcing a decision and forcing vaccinations have an extremely low chance of causing harm to the child being vaccinated whereas banning abortions have an extremely high chance of causing harm to the woman.

The chance of a child dying from a vaccine preventable disease in the United States is far lower than from a car accident. It would be absurd to suggest we charge vehicle drivers with attempted premeditated murder because there’s a risk they might kill people on the roads they’re driving on.

(Yes, I’m aware this is due to herd immunity. I’m not talking about hypothetical situations where the majority of people do not voluntarily get vaccinated)