How are they going to audit? How can they determine whether or not someone's religious belief is sincerely held?
I can not speak for Millcreek's organization, but from the FRAGO I've seen for DOD, requests for religious exemption have to go through a Command Chaplain who conducts an interview with the soldier requesting an exemption, looks at the soldiers immunization history, and then makes a recommendation to the approving authority on whether or not to approve the request.
So, Yes, they are going try and determine if it's a sincere belief or an excuse, as well as (I think) if the person is correctly interpreting what they claim is their faith.