This case has gotten a lot more interesting in the past few days. The new information about the extended flight path is perplexing, but doesn't necessarily point to deliberate human action in my mind. At first glance it would seem to be on purpose and under human control, but here are a few things to consider:
1. There is no logical reason for a human to decide to take that plane to 45K'. The speculation has been that this was to knock the passengers out, but it would be completely unnecessary. The pilots have direct control of the pressurization system, and could easily depressurize the aircraft at 35K' and have all passengers unconscious within about 2 minutes max (and dead shortly thereafter). By the way, I've heard and read all kinds of numbers about the amount of time the fight crew would remain conscious after explosive depressurization at 35K'. "Time of useful consciousness" is considered to be 30-60 seconds at that altitude. Here's a chart:
http://expertaviator.com/2012/04/19/oxygen-requirements-time-of-useful-consciousness-and-intercept-procedures/EDIT: Time for passengers to become unconscious would be about 2 minutes + however long the emergency oxygen masks supplied oxygen (which might be slightly shorter at 45K'). But that's still not a long time because it's expected that after accidental depressurization the pilot's will immediately start an emergency descent to a safe altitude. The oxygen generators don't need to have a lot of capacity.
2. The spread in airspeed between stall and mach buffet is less than 10 knots for that plane at that altitude (it is often this small spread that ends up determining service ceilings for jets). Go below the low end and you stall and possible spin etc. Go above the high end and you hit mach buffet which can quickly destroy the plane or result in dramatic loss of control. It's nearly impossible for a well trained, skilled pilot to keep the airplane within that tiny spread - especially as it was climbing because the numbers change with altitude. That means if it went to that altitude, it probably did so under autopilot control because only an autopilot would be likely to succeed at it.
3. The one bit of convincing evidence would seem to be the "Good night" declaration by radio -after- the transponder was already off. But this is a bit fishy because if the transponder had been off for even a minute before that call, ATC would have noted it, and would have queried the pilots about it when they made that last call. Yes, it may have just been human error there. Most aviation accidents result from a stack-up of at least 3 human errors.
I heard a former 777 captain discuss what he believed was a plausible scenario on the news last night. Basically, he thinks it was all about a slow burning fire which took out avionics systems one by one in slow succession. This has been known to occur before (in other aircraft - not the 777). The smoke may have even incapacitated the pilots before they even knew it was happening. He stated the 777 (and apparently most Boeing aircraft) is designed to tolerate/survive an extensive fire in the avionics bay, and that it would eventually burn itself out without spreading to other areas of the aircraft. The fire may have already started, and taken out the transponder before the "Good night" call, but the pilots weren't yet aware of it. That would be a bit of a coincidence in the timing, but this whole event is something like a 1 in a million occurrence, so coincidences can't be ruled out.