sp3ctre
I just don't see how you can "fix" the problem of a pilot wanting to down a plane. Sure, you could bring in measures to make this particular situation less likely, but what is to stop a pilot in control of the aircraft stuffing it into a row of houses (or the airport terminal) on descent.
Automation.. I know this isn't the most popular answer here, but A/C can (and I am sure they will) get systems that will prevent any
single human factor on the flight deck to pose an immediate threat to the plane, either intentional or not. Where the FCS will simply not allow to be flown into terrain or outside of normal FE.
As such a system could have unwanted side-effects in case of emergencies, there should be an override option. But it's easy to come up with an system/procedure that can be operated quickly and intuitive but physically requires two people - or maybe even disables automatically upon a mechanical or environmental emergency.
The two-man rule is a well-known security measure and such a system will at least require two people conspiring to crash the plane or make a conscious decision to override the FCS protection for some good reason.
IMHO, door locking procedures should be revised as well. There should always be a way to get back in, possibly requiring ground clearance using a comms system from the cabin that cannot be overridden from the FD. From the ground, the decision to authorise opening the door in this case would have been easy: unauthorized descent, no contact with the flight deck and a captain standing outside wanting to get in.