The tweak to the flight control laws that damps the phugoid oscillation seems wholly irrelevant to the Habsheim situation. It's also seems irrelevant to Bilbao. A control input to ensure the smooth gain of height on a 20s timescale isn't going to put someone into a hole they're flying towards.
"due to atmospheric disturbance"… then including the tweak to the flight control or otherwise won't stop it. It's not going to make the oscillations worse.
At Bilbao, if the aircraft is being pitched around so that it enters a protection mode, then it's possible that at least briefly it needed protection - not smoothing the flight path, but avoiding stall. This might have caused it to impact the ground, but what if it had been allowed to stall and crash instead?
Is it wise to fly either into a forest, or into horrible record-setting windshear? A non FBW aircraft wouldn't help you in the circumstances either, unless you recognize the impending doom early enough, and maybe the A320 improved the situation in terms of reducing the number of pieces of wreckage to sift.
Would it be possible to argue that without a yaw damper someone might have squeaked themselves out of a particular sticky fix they'd embedded themselves into? Overall, is it a bad thing to have this mechanical protection?