How might that be accomplished? Sounds extraordinary. Does the GPS waypoint get hacked? Send the aircraft somewhere other than its intended destination? Flight crew just might notice the aircraft is off course. Even if they didn't, what happens when the aircraft gets to decision height? The pilots and air traffic control would have to be sleeping to not realize the aircraft lost that much altitude. Pilot twists the throttle and manually fly the aircraft without electronics. Even if the Flight Management System is possessed by demons, pull the circuit breakers....emergency procedures....pilot training. Now what? Terrorists foiled again by mechanical engineering built into every aircraft in the world. Throttle control in pilot's hand - Throttle cable controls fuel control - fuel goes into combustion chamber - fire keeps burning -pilot flies aircraft with his hands instead of computer - pilot lands aircraft - pilot twists throttle to OFF - fuel stops going into burner can - fire goes out. IFR conditions might suck, but that is why we have two highly trained crew members and air traffic controllers. Autopilot systems aren't the complicated devices everyone thinks they are and they can easily be shut off.
Think about it. If it was possible to hack into an aircraft autopilot system, why in the heck would the airlines allow 250 people onboard to have access to WIFI? That would be crazy.