Wow if there's that much difference between sibs and she still has not grown, I would have concerns myself. Runts often are small because of underlying health issues, as others note. I also would not trust the breeder's vet, especially if this is not a reputable health-testing show breeder active in their regional/national club (ACKCSC or CKCSC -- and I'd expect cardiologist certs (not vet heart certs) for both parents and ideally grandparents, as well as hip scores, eye tests, ideally MRI screened parents of at least 2.5 years old... there's basic guidelines to finding a good breeder in the Library section on the site here
).
It is quite common for vets to just rubber stamp puppies for some breeders that focus on the pet market in particular and pocket the money they get for clearing large numbers of puppies for such people, that is why I'd urge caution in believing what the breeder says her vet says unless she is absolutely reputable and respected. I have the records from a court case in which the judge found against a puppy broker in New York named Marie Larkin who runs Celtic Irish Puppies and where the judge cited her vet as being equally culpable for obviously just okaying health certs for puppies that he knew were ill.
If I were looking for a healthy family puppy with the best chance of a long and healthy life I would never take the runt. I would feel if the breeder is trying to sell you this puppy at full price, it would also be time to run the other direction.
Unfortunately too a lot of unscrupulous breeders try to sell undersized dogs and runts as an attractive feature, knowing that most people will not guess there may be health reasons for the small size. I just rejected a registration on the board last night from a trash breeder, who was, in her internet ads, actually highlighting the tiny size of the runt in her cavalier crossbreed litter as a *feature* :sl*p:. These people make me ill and directly contribute to the decline of so many breeds and the unhappiness of families who buy these dogs and only have terrible problems.
I think the answer you will probably get from most here will be the one you may not want to hear: taking all into consideration and how many unknowns come into the equation immediately simply because of her small size, this puppy is not the best choice for future happiness.