please go with your instincts. YES, the rabies was given too early to her, and YES, she is a very small Yorkie. I would not spay her at this time, she is too tiny and young.
I would also be looking for a new vet if I were you! my baby is 9 months old and about 8 lbs. I have not spayed her yet, and wanted to wait until about a yr old even for her.