A couple of things I learned doing airplane movies:
First of all, the autopilot on a Boeing jet is so straightforward that you could teach someone to set it in 15 minutes. If they had the heading, altitude and airspeed written down, anyone could do it.
Second, I must admit that I do not have a clue about what it takes to turn the transponders off in mid-flight, but I do seem to remember that they are held in by a few screws, and that anyone with a screwdriver could remove them entirely.
Here's a 777 cockpit, if you are interested, showing the autopilot in the center just below the windows, and the transponders aft of the throttles, between the seats.