While the AFOS had it's own AI, its decisions were definately based off of Sara's interpretations of what was going on. While she was in a trance state while pilotting it, she was still in control.
It'll be interesting if the AFOS actually does re-appear in Macross F. Maybe the bio-weapons attacking are something akin to the buster corps in Diebuster, pieces of a larger AFOS system that's there to issue a final test.