Why are we arguing here about who has the correct belief? Intelligent people disagree.
It is completely intolerant to say that the girl should be forced to change her beliefs. How is that any better than her saying that her father should change his? It is the exact same thing. If you think there is a difference, you are simply saying that you align with his belief instead of hers.
To say that he should get full custody just because the mother is a Christian is saying that the government should be fascist enough to restrict religious freedom. That is a very scary thought. Imagine a world in which you have to renounce your religion or your children will be taken away. I don't doubt that it very possibly will happen in the not-too-distant future, but it makes me incredibly sad.