If a judge ever decided what was permissible religious doctrine for a child, we would be back in the days of the Inquisition. Judges have no wisdom in this area. There is no societal consensus concerning what is a proper religion. One person's indoctrination is another person's valued zeal. I would so much rather have not been raised a JW. There are far worse monsters than JWs though. Law does not equate with justice. It rarely rights societal wrongs. The ACLU and NAACP Legal Defense Fund cases are the exception to the rule. What law can do is balance competing ideals.
Keeping government out of religion is a much more important principle than which religion a child is raised by its parents. In this particular case, the child will be exposed to a mainstream view of Christianity. His life will be more diverse than my life was. When I talk with worldly friends, it strikes me that almost no one I know follows their parents' religious ideals. College and life experience made them independent. New York has its own mix. When you must interact with someone, it is difficult to believe they are the devil. I recall seeing ethnic immigrants as a child. They looked nice. Many children refuse to participate in their teen years. It is not easy. I ache for the child sitting through boring meetings. Of course, I've attended boring Anglican services.
Are you aware of the history of "best interests of the child?" The traditional rule for centuries was the ten years doctrine. Women only were granted custody during a child's tender years, preschool basically. Women were considered inadequate to train and teach children beyond that age. The father received custody for the rest of the child's life until majority. There was no discussion of parenting skills, religious choices, etc. Some parents would fight each other with reports of sexual immorality. No one focused on the child.
I could never be a family court judge. The wisdom of Solomon in the Bible with the true mother choosing the child's life rarely happens in real life. There has to be an interesting story behind the no field service concession.