In the series, the real Rory slipped through the crack and was erased from existence. How then could the Centurion Rory exist? If he never existed how could the Centurions clone Rory?
The Rory-shaped Centurian was actually an Auton (one of the plastic creatures we see attacking people in Rose, the first "new" Doctor Who episode, as well as a number of old Doctor Who episodes) created by the Nestene Consciousness. The Nestene Consciousness is part of the alliance of races who attempt to trap the Doctor in the Pandorica.
As to how Rory ended up being recreated, the Doctor mentions it in The Pandorica Opens:
"They could have used her psychic residue. Structures can hold memories, that's why houses have ghosts. They could've taken a snapshot of Amy's memories. But why?"
We see River searching through Amy's stuff, finding a book on Roman centurions as well as a photograph of Amy and Rory with Rory in a Roman centurion costume from a fancy dress party to imply this is the case.
So basically, Auton Rory was created from Amy's subconscious memories of real Rory.