River/Melody seemed to be pretty much on her own after she got out of the Silence's orphanage up until she met the Doctor as Mels, so all the tinkering and brainwashing would've been done before her first regeneration as a kid at the end of the Moon two-parter.
I think they were clear that there's more to it than just being pregnant while time-traveling.
VASTRA: Now, I have a question. A simple one. Is Melody human?
DOCTOR: Sorry, what? Of course she is. Completely human. What are you talking about?
DORIUM: They've been scanning her since she was born, and I think they found what they were looking for.
DOCTOR: Human DNA.
VASTRA: Look closer. Human plus. Specifically, human plus Time Lord.
DOCTOR: But she's human. She's Amy and Rory's daughter.
VASTRA: You've told me about your people. They became what they did through prolonged exposure to the time vortex. The Untempered Schism.
DOCTOR: Over billions of years. It didn't just happen.
VASTRA: So how close is she? Could she even regenerate?
DOCTOR: No, no. I don't think so.
VASTRA: You don't sound so sure.
DOCTOR: Because I don't understand how this happened.
VASTRA: Which leads me to ask, when did it happen?
DOCTOR: When?
VASTRA: I am trying to be delicate. I know how you can blush. When did this baby... begin?
DOCTOR: Oh, you mean...
VASTRA: Quite.
DOCTOR: Well, how would I know? That's all human-y, private stuff. It just sort of goes on. They don't put up a balloon, or anything.
VASTRA: But could the child have begun on the TARDIS in flight, in the vortex.
DOCTOR: No! No! Impossible! It's all running about, sexy fish vampires and blowing up stuff. And Rory wasn't even there at the beginning. Then he was dead, then he didn't exist, then he was plastic. Then I had to reboot the whole universe. Long story. So, technically the first time they were on the TARDIS together in this version of reality, was on their w...
VASTRA: On their what?
DOCTOR: On their wedding night. It doesn't make sense. You can't just cook yourself a Time Lord.
VASTRA: Of course not. But you gave them one hell of a start, and they've been working very hard ever since.
DORIUM: And yet they gave in so easily. Does this not that bother anyone else?
DOCTOR: Amy. She worried the baby would have a time head. She said that.
VASTRA: Only you would ignore the instincts of a mother.