Put simpler.
How does religion help in the education of
Maths - It doesnt
Art - It doesnt
Chemistry - It doesnt
etc etc
So why when 95% of the subjects do not require religion as a necessity except religious education itself, should it be a reason to create a divide between one type of child and another, which then could have a knock on effect which later down the line manifests as racial hatred.
The divide only materialises (assuming it does) in those subjects because parents are exercising a right to look at a school in a wider context. A divide isn't inherent in how the school is set up.