IOW, what does "when stall protection became active" have to do with this initial, and ultimately unrecoverable Stall
You are correct, in that protections are lost in alternate law, so my remark was perhaps misleading and I should rephrase my comment to be "inhibited when stall warning became active".
If it had been so inhibited the THS would have been frozen at 3 deg NU. That would not have prevented the accident because the pilot's continued pitch up command would have resulted in the application of full up elevator which is quite enough to drive the aircraft into stall.
It would of course have made recovery easier, and incidentally would have prevented the aircraft from developing a 50 deg angle of attack so the position error would not have gone haywire, the indicated speed would not have dropped below 60 kts and the stall warning would not have been inhibited.
Others (pilots) will have to tell you if and why the pilot was at fault. I don't feel myself competent to comment on piloting affairs.
The THS "system" is retained because it is an integral part part of the basic C* system. The other systems you mention are self contained and separate.