If you let her have the puppies, you run the risk of her needing a c-section or vet assisted delivery and you take the risk that she will not be a good mother. It's like giving a 13 year old child a baby and telling them to take care of it. They are just not ready. Same goes for dogs.
If you decide to let her carry the pups, you need to be sure and see the vet around day 55 for an x-ray to determine whether or not she will be able to deliver them naturally or not.
Let me know if you still have questions.