Amy doesn't remember the Cybermen vs Dalek war in "Army of Ghosts". Which means the Torchwood base in London was never destroyed and H.C. Clements is still a Torchwood front in Amy's reality.
It is very possible that in Amy's reality, the events of "Runaway Bride" never occurred. The Racnoss queen never attempted to revive her children, and never attacked London on Christmas day.
I think it's still the Doctor's home reality though. Churchill knows him, and he's referenced as having defeated all threats to Earth in The Eleventh Hour. So he hasn't gone to a parallel universe.