The First Amendment's Establishment Clause prohibits the government from making any law “respecting an establishment of religion.”
"The Free Exercise Clause implies special accommodation of religious ideas and actions, even to the point of exemptions to generally applicable laws. Such a special benefit seems to violate the neutrality between “religion and non-religion” mandated by the Establishment Clause."
The government, or school, may not impose prayer or other religious acts. Students are not the government, they can openly pray and share their religion.
6 Court cases regarding prayer in school: http://www.newsmax.com/FastFeatures/prayer-in-school-supreme-court-cases/2014/10/28/id/602801/