My guess is they were already dead - harvested by the "drones" and autopsied on to determine the most vunerable points of human beings.
Character stuff aside wasn't the whole point of the episode that that was what the Cubes were doing?
And how did nobody in the hospital notice a little girl sitting there all day every day for a year?
(And how amazing was it that out of all the places in the world they could be they were in Rory's hospital?)
Definitely a case of cart pulling the horse, I think the cube plot was just an afterthought, the villain necessitated by series madate.
Almost could be seen as a satire of the worst of the new era. Evocative but empty imagery like the girl and orderlies that are discarded when done. Tacky cardboard villain behind it all ends up just being typical ugly old dude with hoary sub-Earth Stood Still motivations. Everything is reversed with no consequences (look how much people are worked up the Doctor might have missed six people, we know what Tennant would have said...."I am SO sorry."). Even Brian just sitting around for days until summoned seemed like some a bit of a jibe.
My favorite part is during the Shakri's speech they show Stewart saying "Tell the Secretary General it's not just hospitals and equipment, it's people. Our best hope now is each other.". Sooooo inspiring.
And the Doctor sure hasn't done a good job keeping his identity quiet has he. I have a feeling that subplot will soon be forgotten as well.