I think they knew she was in the TARDIS- the fact whoever it was dragged it to a specific date and spoke over the loudspeaker, suggests to me they can somehow see inside it. I've had a feeling that there's a big, scary, omnipresent being keeping track of everything team TARDIS does for a while now.
Maybe they didn't know it would keep her safe, or maybe they did know, like the explosion was meant to be a Pandorica for River- keeping her trapped forever.