Has he been diagnosed with a liver shunt? What tests were done? What were the results?
Too little protein is not good for his liver. Protein isn't harmful to the liver. It is the ammonia in animal proteins. If his liver is compromised, ammonia will get into his system and cause problems.
He needs high quality proteins that produce the least amount of ammonia. Cottage cheese, eggs and tofu are best as they are not from animals. Chicken and whitefish are the lowest ammonia producing animal proteins. Red meat is the worst and should be avoided.
This is a great article:
Liver | B-Naturals.Com Newsletter
I agree with you about not feeding Hills prescription diet. It is not a good quality food. I went through the same thing when Lady was diagnosed with diabetes. My vet recommended W/D. I read the ingredients and could not figure out why you would feed such garbage to a dog with a compromised immune system.
Have you considered home cooking? There are some wonderful diets in the bottom part of this link. including one from Dr. Center.
Nutritional Support for Dogs and Cats with Hepatobiliary Disease -- Center 128 (12): 2733S -- Journal of Nutrition
Here is Dr. Dodd's Liver Cleansing diet. I know many people who have used this diet with great results.
Liver Cleansing Diet and Milk Thistle