The right thing to do of course would be for the school to cancel any publicly administered graduation ceremony and allow for the students themselves to organize one or more private ceremonies with their parents picking up the costs.
This way, any venue can be acceptable, no prayers can be stopped, and everyone will be happy.
It is always the season!
If it isn't proms, it is graduations or one of a thousand religiously non-neutral issues that all government schools must deal with as politically powerful groups of citizens fight for the hearts and minds of the next generation of voters.
I have a solution:
Shut down all the government schools tomorrow. Give each student a voucher for 1/3 the cost of what it costs the state now to educate a child in a government school. Over the next 10 years reduce the amount of the voucher and decrease property taxes. In ten years expect the parent to take full responsibility of educating their own children.
Yeah! There would be complete chaos for a few years, but parents would figure it out, and charity would step up to take care of the poor.
What we might see is what the U.S. had prior to the 1850s: homeschools, church schools, tutoring by neighbors, tutoring academies in the homes of neighbors, and apprenticeships.