I think it's less about "how much do we take away", and more about "if we automate this, will we train dangerous habits into pilots who use it?"
You don't tech you junior sysadmins to use "rm -rf /" to delete user data "because Unix prevents you from deleting files not owned by you, so it's perfectly safe!" _one day_ that sysadmin is going to be logged in as root.
I have no idea whether the pilot here was trained to let an Airbus override dangerous actions on his part or not - but if he _was_ – _that's_ something that ought to be considered for changing.
We wouldn't let a car manufacturer sell a car with the brake pedal on the right and the accelerator on the left - because no matter how diligently you tell buyers, or how prominently you point it out in the owners manual, somebody is going to mash that accelerator pedal in an emergency expecting the car to stop.