The people who wanted prayer will have a ceremony in a church. The people who don't want to pray can have a ceremony somewhere else.
Win - Win!
The people who didn't want prayer, now won't be subjected to one. The people who did want prayer, get to keep it.
Having a sixth grade graduation ceremony is a tradition and not even a tradition at every school, it's not a law. So, people can start new traditions. Private ceremonies where like minded people can do what they want to do. Think of all the possibilities.
Not to mention, if they don't like the idea of secular public schools...well, they can always build private schools and send their kids there. No one will care if they pray or do anything else. Without voucher funds, of course. People who don't like government interference shouldn't be looking for government funding.
I like this idea. Everyone gets to do their own thing...and no one has to be offended. Many churches, organizations, etc. already have little baccalaureate programs for kids who participate with them...in addition to a graduation ceremony.
I might even start a little company...arrange your own graduation ceremony. Reasonable group rates, discounts for 5 or more students. Some restrictions may apply. Franchises available. (Can't you already see the possible commercial?)