> So, in this sense, vaccination should be an individual choice?
Emphatically: YES. Bodily integrity is something that is very high on the list of things that a person should have a say over. Whether they do it because they are mis-informed, dumb, irrational or religious doesn't matter, they still should have the final say over whether or not they get a specific injection or not.
There are many things that concern the individual that have consequences for society as a whole, in fact, it is very hard to point at a single thing that concerns an individual that has absolutely no consequence for society. And many of those things are regulated to benefit society. But your body is yours and yours alone and that's a good thing even if there are negative consequences for society.
Fortunately the anti-vaxxers are a small minority instead of a large majority so the risk is somewhat controllable and fortunately the only people at risk are those that have not been vaccinated yet (a risk that for many diseases is extremely small) so the consequences for society as a whole are manageable.
If that should change dramatically then this should be revisited but for now I'm pretty happy to support this even though I would never apply it to myself or my children (who, ironically, don't get to chose because the argument isn't really framed right, it's not an individual choice but in almost all cases a choice for a parent about their child...). This also ties in with religious freedom, and as an atheist you might find it surprising that I'm a big proponent of that, I don't believe in any of this but I will definitely defend the right of others to believe in whatever they want, including in things that may make them make sub-optimal choices when it comes to their own health or the health of their kids.
If you start to take away those rights you will end up with a very unhealthy society, far more unhealthy (and unhealthy on a different plane) than the society that has to deal with some actual health issues in a small part of their population.