If you go out from the idea this was a hijack and they tried to avoid being detected by radar, this must have been a pro with a lot of experience flying in the region. An amateur will not know how to fly waypoints to be undetected by radar. As a flight sim hobbyist I would know how to manipulate the autopilot and FMS to fly somewhere else, but I wouldn't know when exactly there will be a gap in radar coverage (certainly not sitting in the back), or where to fly to avoid radar detection. So you have two options:
1) one of the pilots did it
2) one of the PAX was a pilot and took over the plane
In both cases I think it must be more of a suicide mission than something else.