But why in the world someone who takes (unlawfully, let's suppose) control of the a/c would want to follow a route neatly through all those wpts? If he wanted to take it somewhere, it would be more logical to fly direct.
More logical maybe. but not so easy to an unqualified person flying the plane especially if you are unsure of your location after the struggle to take over control of the aircraft. If your 'nefarious' final destination is not in the FMC database and you really don't fancy dead reckoning at night, a bit of advance planning and judicious use of the LSKs will get you 90% of the way there.
I'm not saying that's what happened but it is certainly something to consider.