The Anti-Vaccination Movement

You're right that not all pseudoscience is quackery. Quackery is applied pseudoscience, generally for the purpose of monetary gain. :P

Generally speaking, the point at which you draw the line isn't actually all that complicated, because it's the same line drawn for every other freedom: you're free to do as you wish until that choice harms other people or infringes upon their rights. Mandatory medical checkups are a damned silly idea because not doing them only harms the person who chooses to not get them, and people are allowed to harm themselves all they like. Vaccines are on the border of the area of protected personal medical choices for two reasons: not vaccinating can potentially cause harm to others by way of allowing preventable communicable diseases to propagate and affect those who are unable to get vaccinated, and not vaccinating your child is potentially harmful to them. It's that "potentially" part that causes the trouble, because if you can't prove for certain that something will or will not cause harm then it comes down to a subjective judgment of just what percentage likelihood of harming others with your choice is acceptable and legally protected and what the tipping point is for that choice needing to be constrained.

Dealing with harmful behavior can take all sorts of forms, but generally the method to be preferred is that which is least harsh to the person at fault that also (hopefully) prevents that harm from occurring again. As far as not vaccinating can cause harm to vulnerable kids, the minimal harshness solution that prevents that harm is to completely bar kids from public school if they aren't vaccinated, no religious or philosophical objections allowed. As for the possible harm caused directly to a child that isn't vaccinated, well, the jury is still out on that one. In more blatant and obvious cases of this same nature that have gone to court, such as parents choosing to forgo real medical treatment for their child's treatable cancer or other serious condition, perhaps in favor of faith healing or homeopathy or other things that don't actually work, most often the courts have ordered that the child must be given real medical treatment because withholding it qualifies as child abuse and/or neglect. Some day in the future it's entirely possible that such rulings will extend to vaccinations. I currently don't think that's necessary, but, well, I wouldn't really object to it either.
This we can agree.

How it should be, in my opinion, it comes to the person and their responsibilities for their choices and the consequences should be theirs and theirs alone. Unfortunately we do not live in an idealistic world so we cannot simply hope that common sense prevails among those who in their own mind, regardless of good intentions, their actions won't have any indirect/direct effect on others. As someone who puts personal freedoms above and beyond political ideology and institutional schools of thought I walk a very fine line on this subject. I also do not believe in absolutes or a very cut and dry mindset.

For instance if a parent decides not to vaccinate their child, for religious reasons or otherwise, then their child cannot attend a public school until the rest of the student body is vaccinated. However, the said parent, more often than not, by that time will choose to home school their child or something else. To the point, society is considerate enough to make accommodations or have contingency in place for those who chose a different path, to a degree. Then again nothing is that simple is it?

Ultimately I think politics fucks everything up.