So glad it finally aired so there can be theorizing about the damned kid! (A lot of people at the New York screening were theorizing that the girl is Jenny since Moffat is supposedly the one who wanted her to regenerate at the end of The Doctor's Daughter, and all the stuff with Amy's kid, the 9 month timeline, etc was all just a decoy.)
Well when the Silence command you to do something, you obey without thinking, presumably even if that thing is to kill innocent people like the Doctor and his friends. Surely the Doctor wasn't sure if they would want them all dead now that they know more about the Silence's plan, so getting Canton to round all of them up and bring them to a secure newly built room guaranteed to have no Silence in it at all was probably the best way to plan a strategy and keep away from any military interference. They can't be pursued by an army that already thinks they're dead.