Technically I believe the autopilot is a higher level in the system, and the anti-stall stuff (among others) is part of the lower-level fly-by-wire system. It's sort of like with a car and the difference between anti-lock brakes (fly-by-wire), cruise control (basic autopilot functionality), and autonomous steering to reach a certain location (advanced autopilot functionality).
In any case, you're right that the automation (by whatever name) can already override the pilot in many cases. But it's a really tricky problem because you can easily make things worse instead of better. For example, one reason that Air France 447 crashed was that one of the pilots was commanding the airplane as if it were in a fly-by-wire mode it was not actually in. The plane had already stalled, but he was flying it as if the computers would prevent him from stalling, rather than taking proper corrective action. A proper recovery maneuver would have saved it. This is ultimately pilot error, but automation is a strong contributing factor. For another example, Asiana 214 crashed because the pilot assumed the airplane was doing more for him than it really was, trusting the automation to keep his speed steady, which it wasn't set to do. Again, pilot error, but with automation as a contributing factor.
It seems likely that automation is a net gain when done right, but it requires careful consideration.