My Peanut was 11 ounces at 11 weeks old... she is now 3 pounds, 4 ounces at just about a year old (she'll be 1 year old on April 30th).
I don't think your baby girl is THAT small.... I think the only difference is that all my small ones never had any hypoglycemic issues.... which could be why your vet is probably thinking there may be something wrong with your girl. Some vets have never dealt with the "smaller" yorkies before.
Keep her sugar level up and make sure she eats... hopefully she will be fine. Wishing you all the best....