Right, you can do anything you want with the babies. In fact, you can put them up for adoption as soon as they're born, you don't have to wait for them to grow up.
EDIT: It just occurred to me it might be nice to explain why this apparent "glitch" is happening. It might help you with other, similar, scenarios.
ES introduced the family tree. Animals who are siblings can't breed. The scenario tells you that you need to have a breeding community. But without the original animals, no breeding is possible. That's why 2nd generation animals do not count. You only have two animals that can breed, so if anything happens to one or both, you are failing the scenario's requirements, and you get that "you only have ONE beaver!" message when in fact you might have several beavers.