What about the remote control autopilot?
If you're referring to external control of the aircraft, I see that as very unlikely. The technology exists, and we may not know the full capabilities of such. If someone could and did take over MH370 from another location, I'd think about two things. First, how would the Captain and FO be incapacitated to ensure success? I'd think they'd fight such a takeover in any way possible and do anything possible to signal distress. Second, only a very few nations could even attempt such a thing. I don't know if anyone but the U.S. would be advanced and brazen enough to do it. Certainly is interesting, particularly with Diego Garcia in mind. I doubt it, though.
If you mean the autopilot continuing to fly the altered and programmed route after the pilots had died, then that's possible. I think that would end with the plane in the water.
You have an Air Force background, so fire away if you've got a good theory. I think all of our theories will be revised and the real arguing and speculation will begin once there's been a clear spotting of a plane, or pieces of one, somewhere. This story is going to get crazier, and I doubt we'll ever really know what we wish to know.