With thanks to SKS777FLYER:
For the jet to leave it's programmed waypoint to waypoint flight plan to China;stored in the flight management system; under normal conditions would have required a human to intervene.
1. A pilot could take the controls manually, click the autopilot off and hand fly the jet whatever direction or altitude.
2. A pilot could modify the upcoming legs in the active flight plan to have the autoflight system steer the jet to new waypoints.
3. A pilot could build a second flight plan in the second flight management computer, activate and execute the second flight plan and either hand fly or direct intercept a waypoint on the new flight plan.
4. A pilot could leave the autopilot on, but steer to whatever heading via heading select mode.
OK, that takes care of Nav (i.e. path over the ground/sea). The route followed could all have been input to the FMS and handed to the automatic flight system ('autopilot') at the time of deviation from the original route to Bejing. No further human input to Nav would have been necessary. Everyone on board could have been dead from that point onward and the route over the ground/sea would still have been flown.
However, could a vertical 'profile' to match the claimed visits to (lets assume) 39000ft and 5000ft be input to the FMS, handed to the automatic flight system ('autopilot') at (let's assume, for ease of discussion) the time of deviation from the original route to Bejing and thereafter be followed by the aircraft without further human intervention?
In other words, after input of the profile incorporating 39000ft and 5000ft, could everyone on board have been dead from that point and the profile still have been flown by the automatic flight system?