I enjoyed this write up by Langewiesche, but the one thing that bothered me was the credence lent to the depressurization event without disclosing what if any evidence there is that it happened? Is there some? In the article he simply says "circumstances suggest" by which I assume he means the climb to 40k feet.
1) It seems pretty clear the plane took hours to crash
2) If the cabin was full of healthy, alive passengers, they could have done something during that time. (It's not a certainty, but it certainly seems plausible. Armored cockpit doors aren't meant to withstand dozens of super motivated people, including cabin crew, with literally hours of time on their hands.)
3) Apparently nothing was done, so apparently it wasn't full of healthy, alive passengers.
4) Although a number of things could have killed or incapacitated the passengers in the cabin, depressurisation is fast, reliable, under the control of the pilot, and doesn't require any elaborate assumptions about third parties or deus ex machina. There are other possibilities that have been discussed elsewhere (poisoned food, perhaps), but Occam's razor suggests depressurisation.
I think that's what the author was getting at with the "circumstances suggest". Given what is known about the plane, depressurisation is the most logical explanation for one of the mysteries.