When I took European History in High School we spent almost the entire class talking about reformation. We read about St. Thomas Aquinas and Martin Luther.
In my Ancient History we learned about The Code of Hammurabi, and The Ten Commandments, and early Jewish and Christian cultures (including some of their rituals and beleifs)
No one cried seperation of church and state then.
PErhaps because we were not actually saying prayers. I don't think this was an attempt to indoctronate anyone. Seems more like the kind of Dress-Up and Play Acting that is done in elementary schools (Although this sheds new light on the quality of American Education, You still play dress up in grade 7?).