The big thing that's been bothering me about the hijacking hypothesis is that there's no clear logical motive behind it. This indeed makes more sense than anything else I've read so far.
One might hypothesize that terrorists managed to take control of the airplane and divert it only to have the passengers counter-attack and then in the chaos that followed either control of the plane was lost and not able to be recovered or it was intentionally crashed. Even with reinforced doors it would not take very long for highly motivated individuals to breach them, whether that's the attackers or the passengers or whomever.
I'm not saying that anything of the sort is likely but similar things have happened before.