Guns and schools are all regulated by the states. The individual states have differing views on what is acceptable, and what is not.
In WA, there are situations where you can carry into a school building, without a license, and situations where you may not, even with a license.
As for a school in a church? The building is a church, and it may be also used at times as a school...I don't think that qualifies as a "school" under even the stupid unconstitutional federal law, when class is not in session.
RCW 9.41.280 for Washington State