I personally wouldnt take the whining as just pain. She may be sensitive in the areas of her spay and her mouth. Just like us even when we take pain meds. We can still feel it , just not as bad. If she is up walking around i would say it prob isnt too painful. Has she had a bowel movement yet? One of my little dogs.. A jack russell/rat terrier is extremley whiney after any surgery. Even after getting his teeth cleaned. Untill the anesthesia wears off completely his is very very whiney . I dont think he likes the way it makes him feel. Plus he is more vocal over anything he doesnt like.
But you know your dog best
so if you think its crying from pain, i would put a call into your vet clinic. They may be able to give her something else to help calm her and ease the pain a little more. Have you tried canned food of boiled chicken or something real tastey? Sometimes they are pretty picky when recovering from surgery.