Re: Hey software, get the fuck out of the way!
The Airbus philosophy is that since pilot error is a/the cause of most crashes, it's going to overrule the pilot if it thinks he is in error.
In the case cited above, the Airbus aircraft recognised it had no idea what was happening, so it gave full control to the pilots, it did not overrule the pilots. Therefore Airbus does recognise that it may, at times, be best to leave it to the pilots. It's default mode is to stop the pilots from doing anything stupid (too tight a turn, to steep a climb/dive, etc.) but that can be disabled by either circumstances where the aircraft recognises that it's got NFI, or by manually switching to alternate law 2.
I believe (from memory, could be wrong) the issue was multi-fold:
1) confusing and contradictory indicators;
2) issues with cockpit layout and information feed to pilots (e.g. alarms being set off by angle-of-attack sensors, but that information, the angle-of-attack, not being available on pilot instrumentation);
3) that each sidestick was independent of the other, so that one pilot doesn't know what position the other pilot has their sidestick in, resulting in the 2 pilots providing conflicting control input, but neither of them knowing what the other was doing to know that there was conflicting control input.
4) management issues, whereby clear, concise instructions weren't being given and/or followed by all pilots, e.g. why wasn't it made clear that the pilot in the right-hand seat was now in control and the pilot in the left-hand seat must remove their hands from the flight controls (sidestick) to prevent contradictory control input (tho the fact that this was happening should have been reported by the aircraft, e.g. mechanically (or electrically/haptic-feedback-type) link the 2 sticks).
It really had nothing to do with the software overruling the pilots. There were many other issues with Airbus's software and cockpit layout/information feed to the pilots, but overruling the pilots wasn't one of them in this case.