You seem to be under the impression that the school is sponsoring the FCA group. It is merely using the building. Have you ever been to a school building in the evening after school hours? It is a busy place, many groups are using it and not all are school sponsored teams, clubs, etc.
Even churches can rent the space to use for worship on Sundays, that doesn’t mean the school is sponsoring the church. Our church rents the gym and a couple of classrooms to use for Wednesday night kids programs. Using space is not the same as sponsoring. It is a public building and after school hours it is used as a community center for all kinds of groups.
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.