Snarly - it sounds to me like the Church is still wanting to sponsor the Troop. By all means, contact the commissioners staff - start with the District Commissioner (not the Council Commissioner - it's a fine idea but jumping over the District Commissioner directly to the Council Commissioner is a bridge you don't need to burn).
But more to the point - the SM has absconded with the unit's gear - a unit that is controlled by the CO. You should also encourage the COR and IH to send a certified letter to the Scoutmaster demanding the return of all the unit's gear, as well as any keys he and his family may have to the unit's closet. In that letter, the CO should (after consulting with the local police so that they are informed and ready to act if needed) that they have 5 business days to return all of the gear and any financial records they may have including the check book, to the CO or that the police will be brought in to arrest them for theft.
Yes - you're about to burn bridges with this family - and so is the church - and yes, the Troop will have to be rebuilt, and that can take some time - but ultimately this is going to have to happen if the Church truly wants to continue to sponsor the unit.