It's unfortunate the pregnancy wasn't caught earlier to have the pups aborted.
I don't have much to say about whether or not the vet was negligent - if you're not happy with the outcome, perhaps find a new vet?
Do you at least know how many pups you're expecting at this point? You should be getting an xray to get a count so when the time comes you can be sure momma got them all out and there are no complications... breeding and puppies really isn't for the faint of heart
Hope you'll get the girl spayed asap as well as your boy - unless you're doing full health testing and proving your dogs in some fashion (either working trials, conformation, etc) then there really isn't a good reason to be breed them.