A earthling-kryptonian baby would be of too much interest for Zod. He wants Clark's powers and he would want to know if the baby will have his powers.
Or he can try and use the baby to blackmail Clark. Jor-el is right in telling Clark not to let Zod know about the baby. Clark will have to keep Lois away from him. With the baby growing fast it won't be easy to hide the pregnancy for long.
Andreia