Ethics: Religious Exemption from Vaccinations

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(from NEJM original)

Where I live, the only way to be truly exempt from vaccinating your children as it pertains to school and day care admittance is to have an actual allergy or receive a waver due to religious beliefs from one's physician. As you can imagine, there's plenty of people who fake a deeply held religious conviction in order to obtain this piece of paper.

The other day I overheard a woman asking her doctor about that exemption. She freely admitted that she claimed religious convictions against vaccines so as not to expose her children to what she perceived as unnecessary risks associated with the injections. But now she's worried. Like everyone else, she's hearing about outbreaks of measles. She said measles didn't seem that bad, but she got to thinking about some of the other preventable diseases like polio. This lady did NOT want her kids getting that crippling disease. So she asked her physician if the religious exemption was an all or nothing setup. In other words, could she make her "religious beliefs" a la carte: MMR is an abomination; the polio vaccine is kosher?

Well, praise God!
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I'm not sure what was said in response to this inquiry, but I'm curious to know what you think about vaccine exemptions. I know many are entirely against them. Others will concede that we must still leave room for religious liberty among those who are true in these beliefs. Another might ask, which faith actually preaches this? Important to me from a public health standpoint is the following question:

Is basing exemption on religion keeping people from getting vaccines they would have otherwise requested? 

The ideal is for people to get fully immunized, of course, but I'd rather have them get some than no vaccinations at all. What's your take on this situation now that I've shared with you what some are thinking?