Might the answer not be to have the automatic control system protected by a password system, so that even if wannabes gained access to the flight deck they'd need to know the security code before they could over-ride the autopilot and take manual control? Likewise, under manual control the pilot could be required to input a sequence of codes to the keypad at random intervals otherwise the system would revert to automatic control.
This idea had me in stitches..
Typical scenario
F/O...
"Ok Captain we've had an engine failure in a critical flight phase with the AP connected, we'd better disconnect the AP and hand fly this sucker"
Captain...
"Great idea, now whats the F**** pass code ?"
Password protected Autopilots, I think not.