As revealed in "The Time of the Doctor", the question "Doctor who?" that was being asked (via the time cracks) throughout time & space was being asked in Gallifreyan. It was being asked by the Time Lords, as a way of identifying their home universe, so that Gallifrey could return. The Silence feared that, if Gallifrey did return, it would restart the Time War & all the horrors associated with it. Thus, the Silence wanted to ensure that the question was never answered & that Gallifrey would remain trapped in the pocket universe where the thirteen incarnations of the Doctor had put it in "The Day of the Doctor".