Nebs, possible but I don't think likely. If the article is close to the mark, and the pilots succumbed to carbon monoxide or any other gas or smoke, it IS possible for the autopilot to continue flight, even all the way to it's intended destination if it wasn't altered as suggested in your link. But when the aircraft ran out of fuel the automation would do one of two possible things.
1. It will try and maintain height, but as the speed washed off (no more go juice) it will stall and crash leaving large amounts of debris.
2. It will try and maintain speed, which will require a nose down attitude and cause a decent at best glide speed. But this speed is not likely to be best crash speed (term used tongue in cheek) also resulting in large amounts of debris.
But also, Southace suggested that the flap that was found could be determined that it was in the landing configuration. Automation does not configure the aircraft
If the aliens didn't take it, Im still going with the pilot being the cause. But HOW he did it will remain a mystery until the blackbox and VCRs are found..