The problem here is that it was not Congress that prohibited or endorsed such prayer. Congress is a federal entity while schools were a local entity. Congress has nothing to do with states or local municipalities or how those local governments run their schools.<quoted text>
Yeah, that was after some public schools started to have mandatory prayers, so that (regardless of your personal beliefs) students were forced to "mouth words." Some felt that this was offensive. In two landmark decisions, Engel v. Vitale (1962) and Abington School District v. Schempp (1963), the US Supreme Court found that forcing students to pray violated the First Amendmentís Establishment Clause. Nothing in it kept students from praying. But it did prohibit school or state sponsored prayer.
The restrictions or permissions of local schools have nothing to do with the federal government sponsoring a religion. Again, the intent of the founders was that the federal government not sponsor or write federal laws with religion in mind.