This is all PURE SPECULATION on my part. I know there have been some leaked filming reports that have purportedly given clues about, for instance, River Song's identity, but I've successfully avoided them so far, so if any of my guesses turn out to be right, it'll be a coincidence! However, there are of course spoilers for 6x1 and 6x2, so be warned.
1) The little girl is River. River is secretly a Time Lady, and she has been pretending not to know who the little girl was in 6x1 and 6x2 for some possibly nefarious River Reasons. She is not Amy's child, but the Silence want Amy to think she is. Not sure how Amy's case of Schroedinger's Womb plays into this theory.
2) The little girl is River. River is secretly a Time Lady, but somehow over the course of her life between being the little girl and growing up into River, she has lost her memories of being that girl, hence her genuine ignorance of what's going on in 6x1 and 6x2. She is not Amy's child, but the Silence want Amy to think she is. Not sure how Amy's case of Schroedinger's Womb plays into this theory, either.
3) The little girl is Amy and Rory's child. Traveling in the TARDIS during Amy's pregnancy has somehow affected the baby and turned her into a Time Lady, or given her some Time Lord abilities like regeneration. This baby will grow up to be River Song, and will pretend that she doesn't remember her childhood, for some possibly nefarious River Reasons.
4) The little girl is Amy and Rory's child. Traveling in the TARDIS during Amy's pregnancy has somehow affected the baby and turned her into a Time Lady, or given her some Time Lord abilities like regeneration. This baby will grow up to be River Song, but will not remember her childhood or who her parents are, for reasons yet to be determined.
5) The little girl is Amy and Rory's child. Traveling in the TARDIS during Amy's pregnancy has somehow affected the baby and turned her into a Time Lady, or given her some Time Lord abilities like regeneration. She won't grow up to be River, though -- she's someone else entirely.
6) The little girl is Amy and the Doctor's child. At some point they have slept together or will sleep together and have a half human, half Time Lord baby. For obvious reasons, this baby does not then grow up to become River Song.
7) The little girl is the Doctor and River's child, half human and half Time Lord. The Silence are trying to make Amy think she's her daughter. Not sure how Amy's case of Shroedinger's Womb plays into this theory.
8) The little girl is someone entirely unrelated to either Amy, River or the Doctor. Not very likely, but you never know.
9) The little girl is YOU. You are actually a fobwatched Time Lord, and although you think you're human, you're actually going to open a watch sometime soon and turn into a Time Lord again. Also, when you were a little kid, you had an adventure in 1969 with a spaceman and some Silents.
10) The little girl is Jenny/Susan/the Master/Romana/the Rani/Rose/Donna/Martha/Jackie/Mickey/that horse from "Girl in the Fireplace."
Personally, I'm putting my bets on #3, for various reasons. But we'll see.