Well, in my own world of "fantasy airline ownership,"
I'd probably run that scenario a bit differently. I'd run it like it were a railroad. The "conductor" is the boss of the train. The engineer is only the "driver" and is separated physically from the other cars. Hard for a hijacker/terrorist to get to them unless they can get to the engine, somehow.
Therefore, for larger wide body aircraft (i.e. 777-ish), I'd build it with solid titanium wall between the main cabin and cockpit that could not be penetrated. There would be no access between the cockpit and main cabin, but there would be a bathroom and maybe a small galley on the cockpit side. I would then staff the main cabin with a "conductor" like person who becomes the boss of the aircraft. The pilot is only the "driver." The aircraft "conductor" would handle all disciplinary/safety matters and be trained for that... most likely armed as well like air marshalls are today. The only reason to contact the pilot for something would be a medical or safety emergency requiring a diversion to a different airport. The pilot to need to get on with the FAA to get the diversion approved.
So, to answer the question, the aircraft "conductor" would handle the above situation. I would not expect or want the passengers to get involved unless absolutely necessary (i.e. "Let's roll.").
