David, Under the protection of the United States Constitution, parent A has the freedom to practice his/her religion and raise his/her child according to these beliefs. Also, parent A also has the right to be free to not incriminate him/herself. What this means, in this case, is that no one can be coerced into testifying regarding his/her religious beliefs. (United States Supreme Court, Donaldson vs. O'Connell.) This is a very tricky case. Sounds like it could be full of appeals. However, in custody cases, the child should have a voice...has the judge asked the child who he/she would prefer to live with?
Oh..don't get a psychologist involved. They can do more harm than good, and you will very rarely find a consensus. Psychological opinions are a dime-a-dozen, and the one that you hire, may backfire on you. Play it safe. You love your child, you know your child, you have all you need. Trust yourself and your attorney.