One man's negative externality is another man's positive externality. Mayor Bloomberg took this to an extreme by banning smoking in NYC clubs. All the anti-smoking people were thrilled....and scores of clubs went out of business and good live music that doesn't cost an arm and a leg is hard to find (there are still some places on Bleecker St). Personally, as a freedom-loving non-smoker, I'd have preferred that the ban never be enacted.
The core concept of the Capital Asset Pricing Model is that risk can be diversified away except for that which is idiosyncratic to the firm. Similarly, in a free society, there is a base level of idiosyncratic risk which we CANNOT eliminate...people will drive drunk, commit crime, murder, they will do drugs, overeat, mishandle firearms, listen to Bruce Springsteen, and perhaps they won't immunize their kids and little Bobby may cough on you.
I'm not willing to give Leviathan the power to diversify away the idiosyncratic risk of freedom. It wouldn't work anyway, and it's the first step toward despotism.
Vaccinations are a challenging issue from a moral/ethical standpoint because there are solid arguments to be made on both sides. The numerous cases of devastating epidemics throughout human history are compelling support for the argument that government has a legitimate role in using "invasive" preventive measures to protect the general public. On the other hand, there is a legitimate question about just how invasive the government should be in situations where the disease in question may be more of a nuisance than a deadly threat.
Interestingly, I'm not sure this underlying question is really the heart of the matter in this particular case. There are unique circumstances in a religious community like the one mentioned here -- the issue of "public health" tied to funding instead of protection, for example -- that add a whole different dimension to the matter.