For millions of years nature has evolved living beings by a certain mechanism. As far as resistance to microbial attack, living beings relied on active and passive ways of dealing with harmful bacteria and virus. Then, someone thought to take a more proactive approach and developed vaccination.
Science analyzed vaccination and deemed it scientific; thus many vaccines were created over the years, and the quality of vaccines improves from one year to the next (see flu vaccines).
Nowadays, a portion of the population wants to revert to the old ways of fighting against harmful microbial attacks. I say let them; but, the people that still want to use modern ways of doing this should be allowed to do so, as well.
What this means is that the only way forward is segregation; the children that use vaccines should be separated from the children that don't use vaccines.
Let nature and freedom of choice do what they have always done.