I'm sure there are all sorts of different arrangements made in school districts across the country for building use. Some clubs are associated with the student body, some aren't. Some pay, some don't. I get that. The issue in this story was not building use per se, but that the Principle was running the group which was wrong IMO and in the opinion of the local school board. For the record, I don't think what he did justified being fired.
We did sort of go off a building use tangent though. My opinion is that these public school buildings not be used for prayer groups.
To be clear, you are saying that the principal should not be running a prayer group on his own time? It was an after school group so it was not during school hours.