They would have had to jam all comms because one sat phone on board would ruin the plot. I know that some flight crews carry them.
Incapacitating the passengers is a lot easier than many would think. If the cabin is depressurized and oxygen shut off at high altitude, all of the passengers will be unconscious very quickly (while the pilots "breathe normally" from a separate oxygen supply in the sealed cockpit). And they can be quickly dead if that is desired -- and I think that is exactly what happened.