Not at all - because gay marriage should never be legal as it's morally wrong and offers no positive benefit to society. The same cannot be said for prayer.
Would you condone a public school holding a "Heroin Shoot-Up" ceremony?
The students were not actually doing anything illegal, they were advocating for a change in the marraige laws. Similarly, if students wanted to advocate for a change in the drug laws, I'd support their right to do so.