I do agree, the romantic notion that the pilot's "human authority prevails" is still commonplace in TV shows and movies.
Back in reality however, modern aircraft increasingly treat manual control input as requests rather than direct instructions to the hardware. There is a spectrum of machine intervention from a basic FADEC filtering out potentially damaging thottle settings, to the Airbus that intercepts and interprets attitude control inputs. These systems are programmed with their own ideas of what constitutes acceptable activity, ideas whose "authority" will always prevail over pilot input. To say that the pilot has ultimate control over these machines is, I think, practically meaningless.
As for solving emergencies, maybe these systems already pay their way by preventing many of them from happening in the first place.
I also agree with you that the desire to be in control is part of human nature. But so are human fallibility with repetitive tasks and in stressful situations.