I'll agree that the "pilots aren't the bad guys" scenarios require a catastrophe onboard that prevents communication.
What's your definition of a catastrophe? Can you discount a Stanley knife (or a couple on non metallic garrottes that could have been brought on board disguised as bloody show laces!!) wielded by intruders who managed to get into the cockpit? Either of those would "prevent communication".
I cannot understand how eager so many people are to lay the blame for this tragedy on the pilots.