Easy enough to sort all this malarky out...do like the French and make all schools secular. No "faith schools", no RI lessons, no religious assemblies etc. If parents want their kids to to grow up in a certain religion (or learn about other faiths), then teach them at home.
Incidentally, I love it in situations like that this when people who don't go to church from one year to the next start protesting that "this is a Christian country". Oh, yeah, sure.