Letting people choose to not vaccinate their children will self correct. We'll lose herd immunity, a lot of people will die, and then everyone will know how awesome vaccines are, just like they did in the 60s. Then the cycle will begin anew.
I lean toward valuing individual rights over all else, but this scenario does present a serious challenge to that worldview.
Another contributor to the problem is that people trust science a lot less today than 2 generations ago. They've seen the negative results of a lot of fraud that has been perpetuated under the banner of "science". (E.g. "scientific socialism", the food pyramid, most of psychology, etc...)