if it just went on auto pilot like you say and everyone passed out, the plane wouldnt have done the aggressive accent then plung that it did. that sounds exactly like a struggle in the cockpit and has been the case with other hi jackings when fights break out in the cockpit.
The fact that after this the plane started to follow waypoints but did not make radio contact, indicates the person in control was either a pilot, or had control of the pilot.
As the plane didnt attack anything, but flew till the end where the fuel ran out it shows the persons intention was not suicide, but probably had a mission in mind.
With flight 961, the hijacker had control of the pilot and was forcing them to fly somewhere that they didnt have enough fuel to fly to.