I think this has been answered (sort of). In The Wedding of River Song the doctor equates the falling of silence with the falling of the Doctor. That is, silence falls because the doctor is silenced, prevented from speaking some terrible truth, which if spoken would have dramatic reverberations. The Silence want this terrible truth to remain a secret and thus welcome silence falling and silencing the Doctor is the necessary measure to achieve that end.
We know this terrible truth has something to do with who the Doctor is i.e. his identity. And the secret is probably not that he once broke his promise to help and became the War Doctor, because he was always open about that fateful decision. So if the Doctor is able to speak some other terrible truth the obvious question is why doesn't he? One answer would be that he doesn't know himself but that he senses something is not right and that he is making incremental progress in uncovering what is hidden.
It is noteworthy that the prophecy does not say who asks the question. It is not an absurd proposition that the Doctor himself should ask someone else a question about his own identity. Looked at that way the prophecy starts looking like a directive to the faithful - the Doctor is getting too close to the secret, do what you must to stop him getting any closer. I think that kind of reading of the prophecy yields interesting dramatic possibilities.