I think it's the same thing as intelligence (in the national security sense). You can do lots of things to prevent outsiders from getting in, but if the insiders want to circumvent the protections, they can. Someone has to have "root" access, when you can't trust that person, you are done.

About the only thing I could think of is some way for people to report a problem like this and air traffic controllers on the ground having a way to take over control of the plane from people inside the plane. But that too could have problems (what if the air traffic controller on the ground is the murderous one, and now he is crashing planes that the pilot can't control).

I think it's a near impossible problem to fully solve. The closest thing I can think of is positive train control (PTC) which sets safe boundaries and overrides the operator if the train exceeds those boundaries. In this case maybe the plane simply can not be flown into the airspace around the Alps no matter how much the pilot wants to.