Student rights to free speech in a school are limited. People here label under delusions. Do you think his closest friends want to hear his view? What if he stook up, threw away an approved speech, and announced that JWs are the only source of truth? What if he proclaimed that all short people are stupid and should be gassed to death? What if he mocks Jewish beliefs?
A public school is not a public forum. The rules are complicated.
He has a right to his views but being a valedictorian does not give him the right to a public platform to impose his views on others. What if every student, parents, citizen of a county, country, hemisphere, continent wanted to equally air their views. Notice that during presidential debates, only two candidates are present. There will usually be about thirty on a NY state ballot.
What I don't understand is why the so-called "believers" feel they have rights more than other people. You do not. If he were so smart, he would have submitted his prayer for approval. What he did is a hallmark of a small mind and juvenile behavior. Thugs, Nazis, Klanspeople, Bolsheviks, Stalinists, Maoists impose their views on other. Why can't we live in a civil society.
You don't have principles that are delineated in any way. If he was right, a mass murderer who is bright and earned good grades is right. Facts are important. Principles stand up when facts change. You invent what is appropriate to suit the moment. I personally don't care what you believe. Would anyone here or on the Internet be talking about this man if he did do something so junvenile that they should have pulled his diploma.