The more I think about it, I kind of think Moffat squandered a chance to do something that wasn't so stereotypical or trope-ish when it comes to Dr. Who. A lot of what the theme seemed to be to me at the start of the season was how Amy and Rory were starting to enjoy their real lives together (aside from the divorce part) and that they were getting ready to stop traveling.
I think the better ending would have been at the end of the episdoe Rory and Amy finally deciding that traveling with the doctor was just too dangerous and they should just enjoy their lives together as normal people. I'm sure this has happened before, perhaps with Martha, but simply a scene with the Doctor at the door to the tardis telling them to come on, let's go to the next adventure and Amy and Rory simply saying no. Something like kind of breaking up with the doctor. No memory wipe. Nobody dying. Simply them deciding that's it.
The thing that really rubs me the wrong way is that even during the whole episode and the promos leading up to it were basically "Watch Amy and Rory's last adventure with the Doctor" and Matt Smith basically saying halfway through the episode in an Inside Dr. Who thing that "Oh, you are going to be so sad."
It just strikes of the stuff people complained about RTD for. How many times have we been beaten over the head with heavy handed forshadowing that traveling with doctor leads to tragedy if you are a companion? I just wish it would have been more different than the cheap, bang, you're zapped back in time never to see the doctor again in the last few seconds. There's an entire, giant loose end with Rory's dad that has been pointed out. It would have been infinitely better if Amy and Rory simply chose to give the doctor up. Simple. Mundane. No deaths. No time energy wiping out New York. It would have been way better and more human.