I can't help but thinking that a non-believing child in a faith school is going to feel extremely uncomfortable being there. Also, are parents really going to send their children to a school following a faith they don't believe in. I really can't see that happening.
If you are going to have faith schools, they will promote religious segregation. It's unavoidable. That's why they're a fundamentally BAD IDEA!
Surely whatever faith you want to bring up your children as, you want them to think about the faith and be aware of what they believe and why they believe that. It's a personal thing, not something you just inherit.
Given that, then ideally we want children to see a broad range of faiths and find out what different people believe in order to work out their beliefs for themselves. Surely lack of understanding between different faiths must be playing a part in religious fundamentalism. This cannot happen in a single-faith school.
Individual religious beliefs and education need to be separate. The education system does have a responsibility to show children the broad range of beliefs out there, not just one which it has been founded on.