I don't think Amy is a ganger. I can exactly why you think that, and it does make sense from that POV, but the Silence, in the 60s, and Flesh tech 22md Century. While they have the TARDIS looking machine, do they have time travel? Doubtful.
The Lodger/Silence machine was established as a proto-TARDIS time machine in The Lodger, and they could *easily* have been hitching lifts in the TARDIS since last season without being noticed...