SO, with a few clever programmers and a couple of hundred dollars of hardware and software, they can commandeer a jumbo jet and do with it as they may..........
All this speculation on control of the aircraft is a pipe dream. Professional pilots monitor the heading and course constantly. If there is a deviation of any significance, the pilot can disconnect the autopilot and fly it manually, thus eliminating any outside manipulation of the airplane.
That appears to be the case.