Is Moff cruel enough to separate them, do you think? The boy who waited and the girl who waited? I think we're being set up to believe they die, which makes me think they don't . So being sent back into the past - or even into another dimension - is the next most obvious option, a bit like Rose. Closely followed by the Dallas option - the whole thing being a dream since the 11th Hour (all the references to myths and stories). That would drive me bonkers, though.
Maybe there is too much grief and danger in this story and they decide it is their final journey so they don't lose each other, so they leave the doctor instead. Or Rory's "they killed kenny" run finally reaches its denouement and Amy is left alone, too broken hearted to continue travelling. Perhaps she goes back to Ledworth to start again, unable to live in the house she and Rory shared. It would be a Donna-esque return to the start.
Or maybe like their daughter their physical forms die and they are saved as ghosts in the machine, an electrical impulse that is glimpsed now and again.
Or - outlandish theory time - they become angels themselves somehow.
Maybe in a timey-wimey bonkers way, Amy writes the book she and the doctor read, as she becomes a writer in the age where she ends up after being sent back in time? So rather than a letter, as in Blink, the message from the past is contained in the book they read.
Night all!