Agreed.
They also made large course changes a couple of times, which isn't consistent with an incapacitated crew unless the FMS was programmed that way. But if they were diverting to an emergency field they wouldn't have programmed a zigzag routing.
I think the least likely is pilot suicide. Theft, flight deck fire, and hijack are all plausible. As well, an “accidental” shoot down by one of the countries within 7 hours of KUL.