You don't understand Family Law. This is a dispute between private citizens and not a dispute between the State and an individual.
It doesn't matter if religion is part of the mix, the court has jurisdiction, just as they would have jurisdiction over a dispute over whether the child was going to go to a fundamentalist Islamic madrassa or a public school if the Father was a christian and the mother was a fundamentalist Muslim.
If the mother were a fundamentalist Muslim who wanted the child to go to an Islamic Madrassa and the Father who was a Christian convert wanted the child to go to public school, how would you rule?
In favor of the parent who has custody.