Religion has yet to be allowed as an excuse for parents abusing, neglecting or otherwise failing to promote the well-being of their child. I don’t think we should start doing so now.
Contrarily, it always been used as a justification for treating children differently for years. Wisconsin v. Yoder said the Amish do not have to send their children to school past eighth grade. I don’t know of any challenges to allowing children to stay home on religious holidays. Many states have religious exemptions to mandatory immunization programs. Many states have explicit religious exemptions to their medical abuse laws. The question is how comfortable we are having the majority trample a minority’s freedom of conscience because we think we know what’s best for their children.