The doctor was saying the baby was stable enough to transport to another hospital, which doesn't contradict the assessment that the baby needed prompt medical care that his caretakers were unjustifiably fighting against. (The baby may have received some immediate treatment that made him safe enough to transport, but not ready to leave hospital care.)
I believe the references to CPS foster parents by the doctor were about the transportation and stay in the hospital, not to immediately discharging from the hospital into a foster home. So the child was stable enough for transportation, under the watch of CPS and also medical professionals, and there was reasonable concern that the child would not get the treatment it needed if discharged to the parents right away. I don't believe there's any contradiction here, in the actual statements, rather than the distorted versions from Bundy.
The baby was returned to its family after approximately a week. That doesn't prove it was totally healthy all along and the parents did nothing wrong. It suggests CPS didn't have a strong case the parents would endanger the baby in the future. Maybe the employees didn't want Bundy followers stalking them at their house, like they did to hospital workers.