Sounds like a completely normal reaction for a dog in pain that hasn't had a lot of desensitization to handling.
I train my dogs from the get go that I can handle them in any way and it's extremely positive, so that when one cuts their hock wide open on ice at the park, I can take him inside, roll him over, clean out the cut, cut dead skin away, apply crème and wrap it without so much as a disagreement, and without help from anyone else- with a dog party in the next room over.
I'd just get her checked out and don't take it personally, but start handling her more when she's better with yummy treats as a reward.
Danielle, owner of...
Fraggle Rock Collars
Fraggle Vom Richcreek CGC CA
Red Dog's Reconnaissance Man CGC
General Patton Vom Winter Storm