That is so sad. I find all of a sudden it is my mission in life to tell anyone who asks NOT to buy a puppy from a puppy store. And believe me, with Rocco, I get asked a LOT.
Yorkies and other purebred dogs have enough health concerns already without having to worry about being from a puppy mill. If you can't get your money back and you still want a puppy, go with a mix, maybe? You might get a healthier pup as there is less chance of inbreeding at the puppy mill.
If you want the Yorkie, buy her, and you will be saving her! Just remember that she needs lots of care and everything is meant to be. Maybe you were meant to be this little yorkies parents!