I've worked with school systems before requesting use of facilities on Sundays for Church plants, or Churches without a building. My impression is that Principals and VPs typically are walking a tight rope, with no actual school board guidance as to what is right or wrong. So they make the call based on their own convictions. In my cases, one Principal would claim separation of church and state and reject the request, but then their replacement would treat it like they would any other community organization that wanted to rent the unused space and approve it - removing the "religion" question from the dialogue.
In this case, I would not be suprised to learn that the school admin really is operating without guidelines from a school board. They made a personal call, feeling empowered to do so in the absence of any other leadership, and thats a scary and dangerous place to have idealogues. If every other school in the district enforced the same thing, citing a reference from the board, then go at the board. But I'm guessing thats not the case here. We the people get what we inspect, not what we expect, and they will get away with whatever we let them.