I wonder if you might be able to get somewhere by subverting some of the expectations of disability or body horror - maybe subverting some of the expectations that might have ableist implications, or even challenging ablistic themes. Changing just one of "what the disability/change is" "what it looks like" or "how others react to it" might be pretty interesting and still let you keep the theme.
Yeah, that sounds really abstract. I was thinking, you mention using certain changes or disabilities may be problematic because they reinforce certain kinds of social expectations or judgements. If there are changes to a person's body that aren't "usual" disabilities, or have (perceived) tradeoffs, that might change, well, quite bit. There is (I think) body horror in being something one had thought poorly of being, which it sounds like you're seeing may be problematic, but also body horror in, say, loss of control or threat to identity, or in differences to how others react, and those might work to shape the scenario differently.
Concrete examples, I think, would help. So, you worry that making a character suddenly obese (and that it is a source of horror) may have poor implications about certain body types and their societal perception. If you make a character suddenly thinner, though, that could have a very different set of implications. One suddenly becoming thinner may still have issues with the lack of control, a nonconsensual modification of their body. Or there may be other changes going on, like a loss of strength (less muscle mass, less leverage). Maybe the newly graceful and elegant hands lack strength of grip, or heard-earned [craftsmanship] skills, leaving their person fumbling or suddenly clumsy. And this kind of change is still a threat to identity, that they no longer look like themselves, can no longer fit what they had been or what they could do.
There are plenty who would see losing weight as a positive, especially a transformation from someone on the heavier side to a body that is more coveted... and, well, that can also play into a kind of horror. Maybe that leads to the inclusion of the horror of, how do I say it, nonconformity (that others don't see or understand them, the lack of communication, lack of sympathy or aid, and other alone-in-the-crowd stuff which is also, I think, a kind of deep and widespread horror).
Another example might be someone gaining an ability, but traumatically. I think I've seen this more with unnatural abilities, but someone developing a natural ability they had lacked might still tap into some nicely horror-ish themes. So, say, someone who was blind is now gaining sight. It can be gained traumatically (something like non-consensual experimentation or supernatural interference etc, etc.) Or its gain can be paired with other losses, perhaps the whatever that is giving them eyesight is also interfering with other senses, ie, the sharp hearing or well-trained touch that let them navigate the world with confidence before, and that loss can be very disorienting because it is still damage to how they see the world, and their own skills that they had thought they could rely on. Or else the acquired sense is itself traumatic to them, one who was blind for a very long time or born blind might have very little reference for how to use this sight, it may disorient them or interfere with their sensory feedback in other ways - maybe to them it feels like suddenly hallucinating with all this extra input they don't know how to interpret.
Other kinds of bodily changes can be perceived neutral to perceived positive, and still horrifying to a person changing against their will, or coupled with other disabilities or "tradeoffs" that the person would never accept as fair trade. And, you can play a "lack of help" or "lack of understanding/sympathy" theme along with this, it kinda makes sense to me that the fears of the body failing or being consumed would be right there with the fear of a lack of help, lack of care, lack of understanding.
Another possible option might be more than one transformation - having paired or even sequential transformations that, um, point in different directions should also help make it about the (non-consensual) change, not about the direction the change was in. Someone being made obese, and then they (or someone else) being made boney-thin, would make it less about obesity-as-a-horror and more about alteration-as-a-horror. Or one change to make a person old and infirm and another changing to be younger and then being patronized, controlled, or otherwise deemed incapable (rightly or wrongly). Changing skin colors/ethnicity or other minority traits could become pretty interesting with more than one transformation, in more than one direction, and you can get a lot of "not-me-not-my-identity" horror rather than a judgement-on-being-that horror... especially if everyone changing comes out the worse for it one way or another.
I can't think of example subversions for the body being decayed or consumed at the moment, but it might still work to include tradeoffs, whether perceived or real and irregardless of if character thinks it's worth it. Or paired horrors with one transforming as doing, one transforming as being done to, and horror from both. This sort of thing might work to make the message complicated, and have your horror subverting instead of reflecting real-world injustices.
Ah, but a lot of this will depend on your style and your intent, maybe none of it fits what you want to see or do in your world, maybe the kind of inversion I'm describing isn't where you wanted to go. You might be able to find some different points where a change or reversal can offset what you don't want, and let you keep what you do want, it may just take some thinking and trying out different contexts.
I hope you find some of this rambling useful :)