Right now the deformity sphere only pairs with disease sphere directly, but indirectly tends to be paired next to murder or suicide a great deal. This is trope-y but also pretty unfortunate; especially given that Dwarf Fortress has such a robust medical industry already implemented and a stated commitment to avoiding player eugenics. Maimed dwarves and those made chronically, even terminally ill, by forgotten beast expulsions feature prominently in DF lore, which is something very few games are willing to portray at all. Making it a few logical steps from sick to evil is pretty far from where the game has gotten with its social model, so now that you're shaking it up I had a few suggestions.
1) Make beauty/deformity in myth translated differently based on the society talking about the myth. This one is pretty obvious, but should become even morseo as generated creatures come to resemble each other and resemble humanoids less and less.
2) Let myths generate with deformity/disease tied to other social expectations. Having body parts or affects from illnesses resembling a deity; or having a deity of sickness and sacrifice also being one of rebirth and knighthood make for more interesting and subversive stories.
3) Positive social roles in societies that have disease and deformity sphere values. Having only sick people be doctors is probably a losing bet, but only allowing doctors already affected by a plague, or immune because of having something else, to treat people that have that plague is good writing. People living within social layers of society they otherwise can't access, passing messages out, maybe becoming disaffected or banding together with ill refugees against old peers. People being given story teller/scholar status to accommodate for bodies that can't fill crafting or combat roles is another example. Players already do this instinctively, but it's also the myth about Cerridwen and Morfran.
4) More plant, rebirth, and animal associations for disease. Illness is often the product of robust life. Even forgotten beasts don't show up before there's a few warm dwarven bodies to feed on.
5) Witches. Witches. Witches.