Henry
Autoexreginated
I agree wholeheartedly about the discussion ahead of time in a session zero.
Making a change like bringing back all the eliminated races? That's something that would have a much larger impact. Just the gnomes? Or even just one gnome? Not so much. Perhaps it does diminish Nibenay to some extent, but plenty of the sorcerer kings failed in their genocides. I don't really think much less of Borys because dwarves are still around. And do the PCs even know about that? And is there some way to make the gnome present without making Nibenay having failed, if that matters to the DM? Perhaps a mutation by the Pristine Tower? Pretty simple, and using an element that already exists in the setting.
I can actually imagine MORE horror if one gnome had survived, via due to a ritual, or a magical stasis (or literally the Imprisonment or Temporal Stasis spells), to come out of stasis in Athas to find that they are literally the last of their kind. Like the Rip van Winkle/Captain America/Connecticut Yankee trope, they are haunted by memories of verdant oases, small and poisoned but still existent streams, small gatherings of their people playing and having fun, and every bit of it is gone and every reference point they ever knew gone, depending on the kindness of the strangers (PCs) they find themselves with.
Then imagine Nibenay finding out that a gnome still LIVES? (maybe after about 6th or 7th level or so, when the PC has sufficient skills to protect themselves and successfully run or hide) Imagine the hunter's desire after finding out that you didn't, indeed, catch every Pokemon? And imagine the role play possibilities in dealing with that, and finding what you could offer the Sorcerer-king to stay his hand, or seeking the resources to thwart the Sorcerer-king for good, if your campaign goes that way?