Equip external doors with code-compliant hardware and secure them when the facility isn't occupied. A simple locked door could be the deterrent that saves your congregation from experiencing arson.
The hardware used to lock windows can sometimes be easily forced open using a credit card or other tool. The best type of window hardware has spring-loaded bolts that insert through the window frame into the wall frame.
Limit and track which members of the congregation have keys and alarm codes. Set up a schedule to routinely change the locks.