Why would they be alienated? There is most certainly room for non-religion in a class about religion. If that wasn't the case, we wouldn't have multi-page religious threads on boards that are filled with atheists and religious nutters. Let it be heated if it must. And at worst, it will be uninteresting, much like any other given class in school if you're not interested in the subject.
Public school is not the Internet. If you don't think there won't be severe cases of alienation depending on religious denomination or lack thereof in a public school (especially in various parts of the continental United States), you're being naive.
Again, did you ever go to public school?
In a perfect society, would I love religious harmony, a complete absence of racism and cultural understanding? Sure.
... but we don't live in one of those, and your solution is not only impractical, but could dangerously erode self-esteem for a few minorities depending on its execution - if not lead to outright persecution. Religious discussion might benefit children to some degree, but it won't dispel ignorance, bad parenting, etc.
As long as parents can preach their religion and imprint their prejudices on their child, bringing religious discussion into public schools is asking for trouble.
So your next solution is to, what, send the parents to parenting school?