Hopefully an autonomous system would be designed so well that no human pilot could think that. See for example NASA's Adaptive Control tech; even if that's made to assist human pilots, the fact that it can actually bring some semblance of control to a plane that has lost function and form in many ways shows what can actually be done.
And as Air France Flight 447 shows, pilots may very well do the completely wrong thing, ignoring every correct procedure intended to prevent disaster.
But the most important, and often overlooked, part of such a system would be that you cannot skimp on the electronics. With an autonomous plane, if there's a problem with frosting over on sensors, you're grounded. There's no 'but the pilot is human so he can fly blind if the autopilot fails'. It has to be 100% reliable, all the time, and with massive enough over-redundancy that the plane would essentially already have to be falling apart into pieces for the overall control systems to fail. That would of course be a significant help to human pilots as well, as it sometimes seems they're being used as an excuse to live with flawed instruments and quality deficiencies in the planes.