My gut tells me that there's some behind-the-scenes going on that we're not aware of. I find it highly unlikely that someone who so brazenly punishes a public school student on religious grounds would reverse course so completely without some more sensible person in a position of authority doing a "U fukn wot m8?"
Somebody grabbed that guy by the collar and told him exactly what he was going to do next: take the blame, apologize, and gtfo.