I wonder if really it is so problematic, or really Hasbro fears some toxic lobby who proclaim itself to be "the voice of the people". If this lobby is unmasked, then we shouldn't worry.
If the setting is going to be rebooted because gameplay reasons, then we shouldn't worry about potentially problematic lore. For example the cleasing war would be replaced with the hunger war, when cities fought each other because by fault of defiler magic lot of harvests were lost, and there isn't enough food for everybody. The creation of the mul wasn't forced breed but genetic engineering.
My suggestion is the size of the Athasian tablelands to be expanded, or at least to show more zones of the rest of the wildspace.
I would add the fraals and the vrusks (PC species from d20 Future/Star Frontiers/Star*Drive).
I would allow living constructs as PC specie, but these also should worry about food and water, maybe because they need an "exosuit" of living tissue to hide/infiltrate among humanoids.
The sorcerers could choose the list of primal or divine magic instead arcane.
"Faithless" paladins would be allowed, because the don't need to pray to any deity.
Monks could be martial artists who fights in the gladiator arenas in no-lethal combats.
The most of times the fights in the gladiator circus aren't with lethal damage, but the deaths are faked by means of psionic illusory effects.
There is hope in the rest and peace in the afterlife, but here the fate of the innocent souls is the Athasian Feywild, the "land-within-the-wind". The Grey is the place for the souls of criminals and sinners with a "bad karma".
The githyankis from Galanaki haven't said their last word. The fact is they have created an empire around Athas in the Astral Sea. You can't imagine what they have created with reverse engineering of lifeshape craft and some spinewyrms.
There are agents of Tharizdum, the elder elemental eye, and other evil cults, hidden in Athas.
Preverser spellcasters can spend psionic-power points to avoid damage against near plants, the effects by defiler magic.
Some Athasian kaijus creatures are worshipped by totemist shamans (incarnum soulmelders).
Some templars are "crusaders" (martial adepts).
The secrets of the lifeshape craft aren't totally lost. The harupex (the D&D version of "biohacker" class from Starfinder). The sorcerer-kings reward their best agents with reincarnations, and the ultimage reward is the elan bodies. Of course the SK want to keep the monopoly of these secrets. At least they allow some items for medic help.
Alchemy would allow the craft of single-use-magic-item with arcane effects.
Most of the spinewyrms are no-sentient creatures, but some are not what they seem and they have got their own secrets.
Sorcerer-kings are enough smart to control by means of deceptions and false hope instead the simple and rude intimidation. The forced works are as punishment for criminals or citizens who couldn't pay the debts (or the high taxes). The worst works aren't for sentient ones, but for "drones", dead movies reanimated by a transgenic variant of yellow-creeper-weed. They are nor undead neither constructs but plants (monster type). Citizens aren't allowed to own slaves (but nobles can "hire" them by means of special taxes).
Wild halflings don't eat sentient beings, but the jerren.
There are bukhas in Athas (PC specie from Sandstorm).
Sorcerer-kings allow the escape of slaves because a wicked reason. They can "gather glamour", and the suffering and despair of the sentient people is like "mana" for them, but also the hope. Then the fugitive slaves who live their last lifes in freedom, they are a "mana source" for the SK althought nobody realises.
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There is an option, a sourcebook style "Sandstorm", with a subclass like the blight prestige class from "complete divine".