maybe just maybe the supposed changes in heading/altitude were just a pilot trying to take control of a major systems/control failure.
It is clear from the path (if the path is correct) they did not have big problems with controlling the jet, they could climb, descend, they could fly perfectly straight and make turns. Frankly the scenario that flight controls are busted and at the same time ALL communications channels are also down while the jet remains airborne for hours is so unlikely that alien abduction is probably equally likely at this point.