The baby could never have been anything other than a flesh substitute as River Song and the Doctor live life in reverse*. The first time they meet (in Rivers timeline) will be 200 years in the Doctors future where River Song as a child dressed in a spacesuit kills him (remember the baby is being raised to be a weapon to destroy the Doctor with).
She's spent the majority of her life being incarcerated for killing the best man she ever knew, unfortunately she only got to know him after she had killed him. Quite a tragic story really, her second meeting with the Doctor must be quite emotional.
* Note River Song refused to help onboard Demon Falls until after the real baby was no longer on the station, and the Doctor never saw the real baby.
I wonder how the Headless Monks and the Silence are connected, who is behind the scenes. Also wonder how it all gets resolved in the end, hopefully not some timey-wimey stuff where it turns out they are just two aspects of the Doctor and the TARDIS is manipulating the timelines to reunite them.