Maybe it's a question of having a system where both computer and human are contending with each other.
Perhaps, but when you disconnect things like pitch trim or autopilot, then the offending system is taken out of the loop. You can even pull circuit breakers to disconnect them.
Now flight controls, that's another issue.
If you lose a hydraulic system, flight controls are usually double or triple backed up with another hydraulic system.
The aircraft (like Alaska airlines) that had jack screws that completely disengaged and broke...well, that's another issue as well.
The article said runaway pitch trim, which is a common emergency procedure that is practiced in simulators. Once recognized and acted upon, the immediate problem is resolved in mere seconds.