"She cannot simply at her own whims enter or leave her religion," Judge Ahmad Fairuz said. "She must follow rules."
This is not about the religions involved, though I'm sure it would be a lot worse for her if she decided to become atheist.
It is about the separation of church (religion) and state. The religious affiliation is printed on their passport, I wonder if it is dependent on the religion of the parent.
Those things should be eradicated but I'm sure that if she's allowed to change and people in general are allowed to change that people will think that it is OK, wrong, so wrong.