Contact an attorney. That principal can't do that. The courts have made it clear that students may gather and pray around the flagpole.
A letter from an attorney should do the trick. If not, further steps can be taken. The new principal at your school simply hasn't gotten the word.
Kids can pray at the flag. It's their right to do so, and every case has been won in court. The principal will back down.
Now, non-students and outsiders should not be allowed on campus for this activity. That's a danger we can all recognize. Even those who pray have been known to be abusers of young people.