The Honest Kitchen makes a formula called Preference that is completely vegeterian freeze-dried raw. You could add your own protein to as necessary to make sure it isn't too much.
For treats, I'd look at something more like frozen peas - something not a protein at all.
I would let your vet know what she is eating. Keep in mind that nutrition isn't something most vets are highly skilled in. It is a very small fraction of vet training. It is also typical that you are schooling your vet on how to treat your baby. Many of them have little or no training with regard to toy breeds. Even though they are still a "dog", toy breeds have very specific needs that are drastically different from other dogs - even the smaller ones.
If it were me and I had a pup with a questionable liver problem and a vet who didn't know much about toy breeds, I would definitely be looking for a new vet. Good luck.
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