The initial reports that the airplane was in cruise in good weather and took 8 minutes to descend and crash greatly reduced the odds of mechanical or system failure in my mind.
More likely, something abnormal had to be going on in the cockpit.
The scenario from the NYT report is at least highly possible.
It's a major pain but there should never be only one person in the cockpit now that we have reinforced doors.
I don't want to go into too much detail but if there's only one person in the cockpit and they're not incapacitated they can most certainly prevent anyone else from entering the cockpit of an A-320 indefinitely. I assume the same applies for other aircraft types.
(I can't think of any way to physically break down the door with what is typically available in the cabin. Those doors are ROBUST!)