In Day of the Moon, the Doctor implants a message in the Apollo moon landing video to kill the Silence on sight.
In Time of the Doctor, the Silence are seen as confessional priests.
Since Time of the Doctor is farther in the future than the Silence, the message to kill the Silence should still be active for anyone who ever watched the moon landing footage (which I would assume would still be taught and shown to humans as it was an important part of Earth history), so why didn't the human members of the Papal Mainframe attack the Silence confessional priests?