Generally the removal of all forms of religion is a good thing, personally I think it should be illegal in all educational establishements regardless of which set of fairy tales they brainwash the children with.
Of course, the church schools make sure they get good results to bolster their vested interests.
Allowing CofE and RC to get away with it has set a precedent - muslims are going to do exactly the same and with these new 'free schools' any number of nutter sects are going to jump on the bandwagon.
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It is of cause difficult to teach history without bringing in some religion . But I watched some lessons in a RC school and they managed to introduce religion into all lessons even a swimming lesson was accompanied by remarks about God watching and that the children should use the wonderful muscles that God had given them.