If SCOTUS rules in favor of the father, that could be interpreted as being the state respecting a religious belief. In this case, respecting a belief in no religion... which is just as much a belief as is having a faith in Christianity.
The daughter is of age to choose what she believes in. She has every right to be baptized no matter what her father demands.
If she were an adolescent claiming to be transgender, the court would almost certainly rule in favor of her "right" to be physically mutilated.
I remember the judge in my divorce over 22years ago saying she wouldn’t tell a 16 yo anything what to do. Daddy couldn’t force her to want to fulfill his visitation rights.