Building on my previous thoughts ...

There have been certain things building up in Rory's character over the last two seasons, a lot of which appear to be parallels to the Doctor. Rory was a healer (a nurse) who became a warrior (a Roman); this is the same progression River accused the Doctor of. Rory has thousands of years worth of memories buried in his head from his two millennia as a plastic Roman soldier, similar in some respects to the Doctor's longevity. Rory is a time traveller and a hero. He has died and been reborn. In his own way, on a smaller scale perhaps, he is an epic figure.

I wouldn't be surprised, after the events of this episode, to see Rory questioning the Doctor's authority more. I don't know if there has ever been a character in a better place to do so. Even River, with all her power and knowledge, does what she's told when the chips are on the table. I could see Rory drifting away from that. He can't fully trust the Doctor, because the Doctor can't promise to always save Amy from the situations he accidentally puts her in. And Rory has learned rule #1 of time travel: the Doctor lies.

I can't properly predict where all that is leading, but it gave me a crazy thought. What if Rory, in his effort to keep Amy safe, slowly turns against the Doctor? What if Rory comes to have reason to become the sort of epic figure that could stand against the Doctor? That could try to defeat him? What could be more dangerous to the Doctor than someone who knows everything that happens to him during this timeframe? What except a parallel of the Doctor could ever hope to oppose him?

What I'm saying is, what if Rory goes on to found the Silence? What if the religion dedicated to destroying the Doctor comes from Rory's need to get rid of him in order to save/protect Amy? In such a case the overall bad guy we're seeing right now would be a future version of Rory. It would give the entire conflict with the Silence a degree of personal involvement that right now it doesn't have. Right now all we know is that there is a diverse group of people with time travelling capabilities who are dedicated to destroying the Doctor. We don't know for certain why they hate him, or how they came together, or how they know so much about him and his past/future, or how they can affect the TARDIS.

This could also fit in with River killing "a good man, a hero to many". Since it's obvious beyond a shade of doubt right now that this will be the Doctor, with River in the spacesuit, then Moffat is probably going to pull something different to surprise us. He doesn't broadcast something unless he wants to pull a fast one. What if it's Rory in the spacesuit? What if the good man River kills is Rory, but she kills him not because she's a bad guy, but because he is? The jail she's in, the Stormcage, is connected to soldiers known as clerics. In A Good Man Goes To War, the soldiers in the Silence army were also known as clerics. Perhaps River is imprisoned not because she worked for the Silence, but because she turned against them and killed someone important to them? But the Doctor wouldn't want Rory dead, not when he would know deep down that a Rory who hated him would hate him for good reason.

I know, that's lunacy. It's pretty much guaranteed not to happen. But I get just enough of a sense from the show right now that Rory and the Doctor are on their way to a confrontation that it makes me wonder. So no harm in a little madness to my theorizing.