If you feel uncomfortable or on edge bolt outta there and find a new vet. If she is handling him rough right in front of you imagine what she would do if you aren't in the room.
Im going to post a link if you want to read it, but be warned its a sad ending, he took his beardie in to have the femoral pores cleaned. You mentioned seeing one is what reminded me. His dragon passed a few days after. He posted pics of what they did to that poor beardie.
This is the link
Hurt bearded dragon ? | Beardie ER | Bearded Dragon .org
My suggestion is if you have a bad feeling dont take him back. Veterinarians are a business and unfortunately their prime goal is to make money, I feel like a lot of the time our pets well being takes tbe back burner.
I hope i don't offend Drache613 but i have had absolutel horrible experiences with vets with my beadies and my ferrets as well. I know not all vets are bad but not all vets are good either.