Even if that WAS the case though ,that would ALSO mean that
  believing we have free will and are responsible for the
  consequences of our actions is _also_ a result of such
  programming... as would be believing we have no choice in the
  matter would be a result of such programming. So, it makes
  trying to figure out "which is which" kind of a moot point.
  Instead, we'd have to go up a layer of abstraction, since
  there's no way for being within the system to see outside of the
  system, as you say. Issues of pragmatics come into play then.
  What's the better choice? (or non-choice, since there's no way
  for us to know which is the truth from within it and there's no
  way for us to get outside of it. Even if an alien species told
  us everything humanity is seeing wrong, we still couldn't really
  see it from an objective perspecive because we'd STILL be within
  that system ourselves).