Actually it isn't as hard as you think. We did delayed vaxed (and have skipped a few altogether) with our son. The first year our ped gave us a medical waiver. After that we had to either get up to date or "look into hearts and see if our deeply held religious beliefs" were that we shouldn't vaccinate. Lo and behold, DH and I looked into our hearts and by George, we had those beliefs. Wrote them up, took it to a notary, gave it to the daycare (who previously had our shot record) and nobody batted an eye. All they cared about was being compliant with the state.
So, I am just saying that even if you have had some shots already, you can still have a change of heart and use the religious waiver.
Now the public schools might be a bit tougher, but even then I think you can stand your ground. Religious beliefs are personal and can change. There is no need to justify them to anyone.