No, prayer in school does not lead to faith-based discrimination, because prayer is free speech. The United States was founded on Christian principles. There is nothing wrong with students knowing the traditions that the founding fathers had. Most Americans are still Christians. There is nothing wrong with offering a prayer in school for those who want it.
I don't believe that people who are isolated to specific schools pertaining to their religion discriminate with others when they get older. Many men and women have been brought up in religious private schools and were very respective of myself as well as others around me. Essentually, the reason school prayer is banned IS because of peoples thoughts on the way the prayers are done as well as who they are praying to.