So a few things going on:
1. Baltar cursing God. Is he still seeing Six? Because if there was one constant with Imaginary Six, it's that she wanted Baltar to believe in God, and follow His teachings. I can't see her being very happy about him cursing God. Is she gone, is that what has him angry? Or is he angry that his vision of himself and Six and Hera going off into some glowing future on Earth has failed?
2. Which leads us to: the children.
Remember that there are prophetic visions involving a Six, Hera, and possibly Baltar.
So it seems the most likely scenario is that only Hera is viable
* Earth-Cylon + human = dying baby (Callie & Galen's son) ??
* Earth-Cylon + Colonies Cylon = unviable baby (Tigh & Six) ??
* so then probably Six ?kidnaps? the only viable human-Cylon baby left, Hera,
the only option left for a sustainable future
That's the best I can make of the signs in 4x12, along with previous prophetic visions.