My vet spays and neuters hamsters, guinea pigs and ferrets. I think if he can do them, a small dog is no problem.   
If your vet is uncomfortable with spaying her, I would not hesitate to seek out a vet more experienced with spaying smaller animals.    
And it wouldn't hurt to wait a bit longer... give her as much time to grow as possible, as long as you can keep her safe. I know many people who wait till a tiny is over a year old, to allow maximum liver growth, as the liver is responsible for ridding the anesthesia from the body. The bigger the liver, the quicker the recovery. You could request a Bile Acid Test to test her liver function.        |