As long as it's government officials in the course of their job and or somebody directly linked with an official government function (like a student giving a speech at the official graduation ceremony), then I don't think it should be allowed.
Often in graduation ceremonies around here there will be events that didn't involve the school at a local place of prayer that many of the students and people around them independently went for prayers and to be together. It worked great. It didn't violate anybody's rights. It didn't cause any trouble, and it was a logical and reasonable solution.
What the fuck? There is no mention of the separation of church and state in the constitution. The first amendment says that there shall be no sanctioned state religion. It allows for freedom OF religion, not freedom FROM religion.
It's impossible in reality to have freedom of religion without freedom from religion. It's similar in the way that "separate but equal" is pretty much utterly impossible in reality and isn't allowed(Yet technically it's not disallowed under the strict wording of the Constitution either. [Don't believe me? Go check it for yourself.] I bet your not going to be in a rush to jump on that are you and allow that are you.)
How much you want to bet if this was somebody that believed in Islam, a Wicken, or even somebody that was a Scientologist or was somebody that thought they were Satanist saying a prayer all those conservative Christians there would be all up in arms and think it was absolutely terrible. It's not their ceremony it's everybody's ceremony.