There are only three ways the state can teach (or deal with) religion in public schools, none of which are appealing. This is excerpted from the 19th century theologian Robert Lewis Dabney:
1) To force the religion of the majority on the children of the minority.
2) A second solution is what the British call the "plan of concurrent endowment." It consists in aiding the citizens of different religions to gather their children in separate schools, in which religious instruction may be given suited to the views of the parents and all paid for by the state alike … It outrages the rights of Protestants by expending part of the money they pay to propagate opinions which they regard as false and destructive, and it gives to erroneous creeds a pecuniary and moral support beyond that which they draw from the zeal and free gifts of their own votaries.
3) The third alternative proposed is to limit the teaching of the state schools in every case to secular learning, leaving the parents to supply such religious instruction as they see fit in their own way and time, or to neglect it wholly. Of this solution no Christian of any name can be an advocate. we have seen how utterly the Pope and his prelates reprobate it. All other denominations in Europe regard it as monstrous; and indeed no adherent of any religion can be found in any other age or country than America who would not pronounce it wicked and absurd for any agency undertaking the education of youth to leave the religious culture an absolute blank. Testimonies might be cited to weariness.