Ah i see what your getting at, but consider this, options in the game can- and in many cases are- triggered by who you have in your party at the time or what specific dialogue choices you make.
Like karlach can become a mindflayer sure, but if you dont have karlach with you when confronting the emporer, does that option and dialogue still trigger? I dont think so (but i could be wrong)
So adding an option to fix her but that requires some set up to get it right* to trigger again really wouldnt be that jarring of her character arc. Atleast in my opinion. The character arcs can change and differ WILDLY through out the game based on player choice karlach though doesnt seem to get that currently.
She's the only one that can be turned into the mindflayer (although I think Gale can offer to blow himself up if you didn't take care of that by then but i'm not sure). That's her special interaction unique to her, if you add to this the fact that she wasn't origin until very late and (i'm not sure about that so correct me if i'm wrong) she wasn't even companion at first, you can see that there is a real possibility she wasn't meant to be fixable and we weren't even supposed to spend so much time with her.
