I guess find a lawyer who knows about these things?
The Federal law in question pretty much bans the possession of guns within 1000 feet of school property, and only makes some limited exceptions for those with permits issued by the state in which the school exists. From what I've read, it doesn't appear to matter if it is a public or private school, or if it is after school hours or school is in session. It may even apply to home schools.
If the church's school is not covered by the Federal law, then you can start being worried about the state's law.