Incidentally, you mention terrorists overrunning a control centre. In what way is that different from them overrunning ATC now and giving out bad instructions to cause a crash?
Hardly likely, though. Even if someone gave out a false instruction via the radio, it wouldn't be easy to cause a crash, simply because there are natural safeguards in the existing system.
Don't forget, there has to be human input to program the autonomous aircraft in the first place.