Run, hide, fight? How can you effectively fight when the head shed has fully disarmed you?
The senior officers try hard to avoid things that are career-enders. Currently, having somebody under their command shooting somebody without total justification, is considered a career-ending incident, so the incentive is to disarm everybody.
Change the incentive structure.
Every time something like this happens, and the base had nobody armed to stop it, then dismiss the entire command structure. Take the organizational chart, and nuke it from orbit.