Amy is crying, but not because she's sad: It's because, for reasons she doesn't understand, she is happy. This is scary for her, scarier for us, but not scary at all for Rory. It's terribly sad, for Rory, but he doesn't know it yet; as much as I'm unsure about Rory's heroicness when all is said and done, I must say that this is the worst thing to happen to anybody in this entire season. It's almost too gruesome to think about, if you think about it.
Because meanwhile, as Amy is stretching herself out into these unknown, time-breaking places where she's happy because she doesn't know why, because she has accomplished the Doctor's miracle, this is what River is saying: "They're all right here in the storybook: Those actual Romans, the ones I sent you, the ones you're with right now. They're all in a book, in Amy's house, a children's picture book."
Because something -- not Amy's specialness, not the magic of the TARDIS, not anything like a miracle -- is using Amy, cruelly, all the pieces of her childhood, all the dearest things of her -- her favorite things, the things she loves most, the things she loves so fiercely she still loves them when they've vanished -- in order to create this trap. The Romans, the Pandorica. So perfectly well that even the lipstick worked on them. So perfectly well they don't even know that they're fake. So perfectly well that a joy rises up in her that is so fierce and full of love it scares her.
"They might think they're real. The perfect disguise. They actually believe their own cover story, right until they're activated."
And Amy is weeping, with a joy she can't name.
As the TARDIS acts up, crazy and frightening, jerking River away from them once again, a fancy dress photo of Rory the Centurion, once upon a time in her hands, and Rory begs Amy to remember him, to love him again -- to marry him -- the trap closes around them all. The TARDIS is under something else's control, here at the site of the explosion, with River inside and the Doctor begging her to break free, or put the TARDIS to sleep, or run out the doors altogether, and the voice of Silence taunting her, and Rory begging her to remember as River fights to get control of the TARDIS again: Somebody else is flying it. Somebody else is in control.
The Romans drop like puppets with cut strings, and rise again. The Doctor can't see them: He's yelling at River to get the TARDIS somewhere safe, before she explodes and makes the Cracks. The Romans open at the wrist, Nestene guns at the ready, as the Pandorica opens. Rory's screaming, up above, begging to stay himself. Begging to be Rory.