This will depend on your state law. However, signing a waiver indicates knowledge of potential liability. Why would you EVER sign up for that voluntarily.
Just state that you will be working on your vaccination program with your family doctor after you take the baby home and thank you very much but you dont have a relationship with the Dr. in the hospital nor with the hospital and your family considers this a family matter that your family physician will take care of.
Then do whatever the hell you feel is appropriate once you are out of that hospital.