"Anything that's connected to a 'network' can potential be hacked into and manipulated / hijacked. However, I remember that it was said that the communication systems had to be shut down by hand. "
true-but where's the network coming from?
If there is no phone signal, no radar, etc then there's not going to be, I dunno, wifi access. And if whoever has done this actually has control of a military satellite, then a. we have bigger problems and b. why they would use this technology to nick a civilian plane is probably the bigger question.
If the passenger is onboard the plane and controlling from within the plane then I would have thought locating the hijacker would be very easy, possibly even doable from the cockpit.
And surely, there will be a way to perform a manual override and, if absolutely necessary, fly visually while calling for help?