Yes, apologies for crossposting/assuming with the ND comment. My experience is ND (DS2 is ADHD probably AuDHD - also massively struggles with anything unexpected) but medical trauma could completely understandably cause its own set of issues. Lack of hunger is not unfamiliar at all here! It is common in children with sensory processing differences, as it is related to the sense of interoception. Kelly Mahler has done a lot of research on this.
I think autonomy is important for every child, but especially important for any child who struggles in any way or who may be seen by the world in general as less capable, and particularly if they genuinely are less capable, because that means that there are highly likely to be more situations where there is no option for them to retain autonomy, which makes it all the more important to protect it where it is possible. I actually think autonomy in medical care is huge, I have a whole thing about it which would take too long to write, but from what you've written, I think you already understand this very well. I absolutely would not force in the situation you describe, but I would try to keep the conversation open, and be keeping a very close eye on whether symptoms are increasing vs improving. Maybe after she is better, it would be something to bear in mind in case medicine is needed at any point in the future so that you have some things on hand to try and it won't be as unexpected.
If you think about the way that (generally good, non abusive) parents tend to use force, or even the milder coercion (bribery, emotional manipulation, threat of punishment) for things like medical care, it is a rare event and as you said, when it is felt to be absolutely necessary. For the vast majority of children that is a tiny blip in their life. They can easily recover the relationship and trust with their parents because the balance is tipped heavily towards safer, kinder, more compassionate interactions and the "cruel to be kind" moments are few and far between and even a child can understand that in context. When you have a child who has a lot more need to endure things which are absolutely necessary, you can't resort to force or coercion for all of it. You just can't because it would not be possible to balance it out, it would be more cruel than kind. But medics (and sometimes teachers) do not always take this into account. They see that parents can force children when something is necessary, and they assume that is a reasonable course of action. It absolutely is, sometimes, but when you're dealing with a more complicated situation then you need a lot more tools up your sleeve which lean towards the kind side than the cruel one. Because you need to save the cruel to be kind moments for when they are absolutely necessary, which is a different threshold to where most parents would be able to draw that line.
The FB post I linked is a fantastic page by an occupational therapist. The whole ethos of OT is about finding ways for patients to do things they need/want to do in a way which works for them with their current abilities, which I think is fantastic. I follow a few different OTs for this kind of thing (Greg Santucci is another good one). TOPT though who I linked to is especially good for autonomy related posts and figuring out communication and paths through where the "standard" or "obvious" solutions don't work.
The Ross Greene method comes from his books, you might find them useful if you have not read them before. The Explosive Child is the most well known one and is aimed at parents with behaviourally challenging children, it could be the most applicable for your situation. There are also various online resources, I like the talks he has done online or on podcasts etc. He is all about using curiosity to find out what is making it hard for a child to do something because often when you find out what is in the way, it is easier to find a way around it which is genuinely sustainable and works for both of you.
Linda K Murphy and her books and website are also brilliant.