The Silents in 1969 may not have known it was the ganger.
We don't know when Amy was switched with a ganger but we know it was before "The Impossible Astronaut". Before that episode it's highly unlikely that Amy was in that period of time.
Alternatively, they might have known exactly what they were doing and kidnapped her to make the Doctor and his friends concentrate on Amy, instead of on the little girl. It was, after all, a very effective diversion.