NASA were conducting unmanned test flights of Boeing aircraft as far back as 1984. By the time of 9/11, widely available technology in the U.S. had brought accuracy of auto-pilot positional data to within 3 meters. All needed from there would be a link between the ground and aircraft to programme a course. I don’t see any great issue in setting an aircraft up with such a link.
There was one B-707 (an old 720 I believe) that was fitted with a pretty rudimentary remote control system, no "datalink" type system which would allow it to use navaids and such. Precise control of the aircraft was pretty rough.
Today's technolgy, with everything so automated and digital, it seems it would be possible to refit aircraft with some type of automation. It would be complex and very expensive, and there's no evidence of such a unmanned control system even being anywhere near a operational state. Maybe some brainstorming, but nothing set to hardware or software.
I don't think it would be a popular concept with the flying public...or pilot's unions...