Bombs away!
Fires in cargo? Simple.
Create "bomb door" compartmentalized storage units each with it's own bay, and simply pull the lever. The loss of some baggage is expected and a small sacrifice for saving lives. With the main conflagration gone, it would also be simpler to address the incidences of crossover into adjacent units, as now there is working room. The technical issues would need to be ironed out. It would call for a redesign of new aircraft of course.