Altho the Establishment Clause is getting applied in a manner far different from the Framers' original intent, the Constitutional protection of the free practice of religion remains in force. This is why there is no law banning prayer in the government schools. This is also why the Native American Church is rarely prosecuted for the sacremental use of peyote (altho, oddly, Lao Buddhist use of opium is not accorded the same dignity).
Occasionally, however, the suppression of religious practice is embodied in laws which purport to have a totally unrelated intent.