After watching The Almost People I couldn't help but wonder if the Doctor had misjudged the Silence.
We find out the Silence can plant subliminal messages in people, which one does does when it first taks to Amy, telling her to "tell the Doctor what he must know, and what he must never know". Now I think that one of those things might be her pregnancy (which she does tell him about at the end of the first episode) which is what leads the Doctor to realise that Amy isn't actually Amy.
So, could the Silence have known that Amy was actually a ganger and that they were trying to find some sort of proof? (After all when they kidnapped her they were examining her, perhaps with that in mind.)
This could, of course be bias on my part (since the Silence never seemed to be doing anything terribly evil and certainly didn't deserve the genocide they got) but it seems to make sense to me anyway. Or am I just crazy?