I am a little confused by your question.....you seem to have answered it yourself - excess protein is converted to amino acids which are converted to sugars in the liver.
Gluconeogenesis - Wikipedia, the free encyclopedia
Too much protein can also lead to elevated blood sugar and or insulin.
Primal Blueprint advocates a balance of carbohydrates, proteins, and fats. Excess carbohydrate intake (particularly in the form of highly processed grains) will drive chronic elevated insulin levels, cause derangement of satiety signals and result in weight gain. It is much harder to overeat a diet that comprised of higher amounts of protein and fats.
How to Eat According to the Primal Blueprint | Mark's Daily Apple