I agree with you in a sense. I looked carefully at the information on vaccinations and their correlation with autism when it came “time” to vaccinate our child. Our pediatrician agrees with you 100% and gave the same reasons. The CDC also is strongly supportive of vaccinations. That said some MD’s and researches do see a correlation and it is the parents call not the school boards.
True that it's ultimately the parent's call -- BUT, given the public health risks, if that's the case then the public school has the right to refuse to register the child. If it's on purely prudential grounds, you can't get a religious exemption (although I might well come up with my own homegrown Religion of Prudence, I suppose). And you can't put the kid in private school because they will demand the immunizations (and since usually there are 10 applicants for every place they don't have to deal with the annoyance). So home school is the only alternative if the schools refuse to accommodate ones concerns. If only one or two kids aren't immunized, they might well work with you -- but if there's a groundswell of anti-vaccination parents, there's going to be a problem.
I think taking out a truancy warrant against the parents is pretty extreme, it shouldn't come to that, but that's how a bureacracy thinks.