I know that the religious exemption is written into law and I know this regulation has nothing to do with that one but I do think it's worthwhile to pause for a momment and consider this difference.

About 2600 programs in Virginia are regulated by these standards. The DSS child day care search has 1522 unlicensed programs. Those unlicensed programs don't follow these standards and yet there are thousands of children in those programs, learning, growing, and thriving. The vast difference between barrier to entry for licensed and unlicensed care creates a huge problem for families, children, and providers. The goal of regulation is to provide minimum standards for health and safety. Yet about 1/3 of the providers follow 5% of the rules the other two thirds have to follow. Is it possible that a significant portion of this document is simply unnecessary, it seems likely. 

Sure there are ways in which I think religious exempt programs could use more regulations but there are a thousand more ways these regulations create undue and unnecessary burden. It honestly might be easier to found a church than operate under these licensing standards and the policing that comes with it.