Glad to hear that your new pup is doing better! It's also good to hear that you were able to get a second opinion. After reading your thread I completely agree with you.
If that had happened to me I would have felt distinctly taken advantage of, whether I could comfortably afford the medication or not. Personally if the bacteria was a known issue and it was reasonable to suspect the puppies would get it, I feel that should have been explained from the start, as well as going over possible treatments and giving you the option from the start of leaving the pup there longer until she had at least gotten a good start on treatment.
I would have no faith in her as a vet myself, even if she is a good breeder. I think you took the right steps, quietly bringing to her attention that she's not acting in the best of faith, and then stepping away from the situation.
Hope your girl recuperates quickly and you two can get on with having a ton of fun!