I've always figured she was the same thing that Head Six and Head Baltar were. Only visible to everyone and unaware of her own status. And Baltar's line at the end when Six calls their boss "god" seemed to suggest that whatever it was, it wasn't god.
You know it doesn't like to be called
So it seems she was the creation of some sort of very powerful godlike entity. I imagined it as something like the ascended from Stargate. Energy being perhaps. And Head Six, Head Baltar, and Starbuck were all probably also similar beings -- only with out awareness of their abilities.
This is of course, total speculation. Which is about all any of us can provide in answer unless some book or interview has provided a solid answer.