Said by a crazy murderer who was trying to save his own life. He could have just been lying. It may have even been part of the GI's plan to lure the Doctor's companions and the Doctor himself to the place where he wanted to exact his revenge.
Erm - I think you're getting things confused there.
Crazy murderer guy: "The Doctor has a secret he will take to his grave, and it is discovered."
Secret = The Hurt Doctor
Grave is discovered.
Interesting thing there is the interpretation of "Take to his grave"... originally you think "Doctor's death"... but maybe not!
Dorium - that's the fat blue guy who has lost a lot of weight - relating the Silence's aims:
"On the fields of Trenzalore, at the fall of the 11th, when no living creature can speak falsely or fail to answer, a Question will be asked. A question that must never, ever be answered."
Fuller conversation:
The Doctor: What's so dangerous about my future?
Maldovar: On the Fields of Trenzalore, at the Fall of the Eleventh, when no living creature can speak falsely or fail to answer, a question will be asked. A question that must never ever be answered.
The Doctor: "Silence will fall when the question is asked."
Maldovar: "Silence must fall" would be a better translation. The Silence are determined that the question will never be answered, that the Doctor will never reach Trenzalore.
The Doctor: I don't understand, what's it got to do with me?
Maldovar: The first question—the oldest question in the universe; hidden in plain sight. Would you like to know what it is?
The Doctor: Yes.
Maldovar: Are you sure? {the skulls start turning} Very very sure?
The Doctor not very very sure: Of course.
Maldovar: Then I shall tell you. But on your own head be it.
Cheers!