I came out as an atheist in 7th grade (shortly before my Bar Mitzvah). I went to a progressive private school. In 8th grade, we had a course that centered on the 3 major monotheisms as a means of teaching a broad swath of world history. We learned about the wars described in the book of exodus (though I don't recall the teacher ever saying that the archaeology doesn't support the idea of a single large exodus, but rather that there were likely many migrations whose stories were later grouped together, along with other allegories, fables, and true histories, by the authors of the book). We learned about the expansion of Christianity into the Holy Roman Empire. We learned about the rise of Islam and the Crusades. It was really fascinating history and in no way offended me as an Atheist or as a Jew.
Learning about religion in that way in middle school I think is great, even if it were a public school. Having courses about the beliefs of religions other than just how those beliefs impact history, however, would be unconstitutional in a public school. You could provide an environment in which it is easy for kids to start a bible study or other religious club, but inherently, offering education on the beliefs of one religion (or even several) that is structured by government employees (public school teachers) violates the Constitution because inherently it discriminates against other religions. Such courses are great in college or perhaps even in private high schools where they are up front in the application process, but they should not be part of public elementary school.