The woman in the White House toilet - the Silence knew her name and was in the bathroom with her - maybe she was "destroyed" because - putting this delicately - she proved she wasn't pregnant.

The Silence impregnated Amy and were watching her to see if it "took". When she felt ill at the White House and went to the loo, they knew the implantation/impregnation had taken and destroyed Joy - partly because she was no longer needed and partly to destroy the evidence or prevent her pregnancy continuing. They also thought that the Doctor was Amy's bloke - simple mistake or lack of understanding of human relationships - and told her to tell him she was preggers but not to tell him about their involvement - hence her "pressing need" to tell the Doctor she was up the duff instead of Rory - she had to tell him because the Silence told her to.

The Silence have been trying to create a TARDIS - they could be trying to create Time Lords too. 1969 - the year of the first two episodes - is also the year (our time) that the Time Lords were first named in Troughton's War Games episodes - in a plot that involved proto-type TARDISes called SIDRATS that could change their internal dimensions - like the flat in The Lodger where the Silence TARDIS-like room was first seen. The multiple TARDISes in this weeks episode - and some other elements - would fit with that episode too. The Silence could implanting "DNA" into humans. Maybe they chose Amy for a specific reason - remember that people who've travelled in time have that "aura" - or maybe they've been impregnating women for centuries and making everyone forget the babies - or failures.

The Silence may be Time Lords or a species placed on Earth to re-create the TL race using TL DNA and human hosts or they could be a Time Lord-like species or off-shoot (think Vulcan v Romulan).

It's also possible that the time we know she was strapped down in that bed by the Silence - which was an unknown amount of time after she saw the Silence nest in the orphanage- was not when she was impregnated/implanted - that was when they "harvested" the baby or foetus. The orphange could be where all such "babies" were placed. The missing children - could have grown up into fully fledged or adolescent Silence - the ones hanging from the rafters - and as soon as that happens, they are forgotten - hence the old bloke thinking they'd disappeared.

Within days of the 1969 moon landing, a number of events happened that have spookily-apt connections to this story....

Senator Edward Kennedy's car crashes into the Chappaquiddick - his female passanger is killed and he claims to have no memory of the event.

Col Gadhafi seizes control of Libya by deposing the king - whose name was Idris

Pioneer 10 was launched to study the asteroid belt

Mariner 6 reached Mars

A load of spaced-out weirdo's got together at Woodstock and started breeding like rabbits.