If the cockpit crew can cut off oxygen flow to the emergency mask in the cabin then just popping the outflow valve open while at cruise altitude would disorient everyone and within a short time ( couple of minutes at 35,000 feet) all would be unconscious from lack of oxygen.

Rapid decompression on top of no oxygen would stop any attempt of a takeover quickly. Throw in some aggressive maneuvering just for good measure and I think the situation would be contained.

The only problem would be to determine who the bad guys are before everyone expires.