This may be wrong but is it possible that the silence were protecting the human race from much worse? I mean if they can plant post-hypnotic suggestions in the mind then perhaps they were keeping something much worse away from earth. Now that the doctor has put the silence on the run, perhaps this much worse thing will come and kill the doctor. Would be a good logic loop. Silence drive astronaut-thing away, Doctor defeats silence, astronaut-thing comes back, kills doctor. The kind of paradox they implied in the last season.