Huh. Apparently I wrote something about the Ponds' leaving (and how they seem to "leave" several times before that point) last year, and never bothered to post it:
I’ve been thinking about the Ponds’ departure, and stories and un-stories. S5 has such a tightly structured arc, in some ways; I mean, it’s generically baggy in the way that Doctor Who seasons are always a bit baggy, because the episodes are so often individual adventures, but emotionally the narrative ties together quite neatly: Amy starts off opposing childhood (magic, adventure, the “Raggedy Doctor” who sounds like the childhood story, the childhood toy, that Amy makes him into) and growing up (marriage), and the end of the season – like “Amy’s Choice” – reveals that for the false dichotomy it is: growing up and getting married doesn’t mean leaving adventure and the Doctor behind. But it’s also true that no one can travel with the Doctor forever, and the Doctor both knows this and doesn’t want to know it, because he loves his companions and doesn’t want to give them up. (Amy seems, often, to know this far better than the Doctor, maybe because she’s waited for him for so long and so often; she’s the one who talks about the Doctor traveling without her: “long after the rest of us are gone,” she says in “The Doctor’s Wife,” and it’s a recurring theme of both the S5 and S6 minisodes, whereas the Doctor says things like “You’ll be there till the end of me” [in “Dinosaurs on a Spaceship”] – trying hard to believe that, at least for the moment.)
Moffat’s on record in interviews as saying that the Eleven-and-the-Ponds story is one about what happens when the Doctor stays in his companions’ lives too long, and it’s possible to see S6 as an answer to that question: his involvement in their lives past their “natural” separation point sees Amy and Rory’s daughter taken from them. So he tries, after that, to let them go, at the end of “The God Complex.” But Amy and Rory are his friends and his family, and Amy is ‘the first face his face saw,’ and so he can’t let them go after all; he comes back, at the end of “The Doctor, the Widow, and the Wardrobe,” when it looked like Amy’s story with the Doctor was finished, because relationships don’t end like stories do. And so, ultimately, season 7.1 winds up feeling formless, because it’s an un-story rather than a story: it’s about characters unable to find a proper ending, because they love each other too much to let go cleanly. If you find yourself thinking that the Ponds could easily have left – narratively, at least – after “The God Complex,” it’s because they could have. But in terms of their relationship with the Doctor...well, Amy was still setting a place for him at the table and listening for the sound of the TARDIS, and he was still picking up the phone to call them and leave them messages, hoping to hear Amy’s voice before facing down some danger. The narrative problem of the Ponds is precisely the (to me) delightful way that they mean so much to the Doctor, and he to them.