I posted this in the other thread but this seems to have more activity so i thought I would see what people think here. I feel it is unlikely that this would be so as it doesn't seem the shows style, but then again the way the show is going every episode surprises me. Although it is far fetched i feel it avoids the whole doctor/Amy having an affair problem.
Amy having an affair with the Doctor does not seem like something BBC or the Doctor would do, is it possible that the Silence used the post-hypnotic abilities to manipulate the Doctor and Amy at one point so they would have a baby but forget about it? This would explain why it would happen and why they don't remember, and Amy did say about how they had been travelling around a lot together as an explanation of why she told him not Rory. This would mean that the Silence would be able to raise their own timelord that would be able to fly their tardislike ships, without the Doctor knowing?