Typically, pups that die when they are born are usually lost due to problems in whelping, not due to the "health" of the pup. If one pup was large and got caught in the birth canal and the breeder didn't get help right away, the subsequent pups ready for birth can detach from the placenta and die because there is a block and they can't get out. And since you said some were born natural and some via C-section, that's most likely what happened. Nothing to do with the health of the pup.
So as long as the clearances on the parents were done and otherwise, you are happy with the breeder, I wouldn't let how the birth happened change my mind.