It’s official now (from some time now) that Amy and Rory will leave Doctor Who series during the next season (season 7). Karen Gillan appeared on October 29th 2011 on Graham Norton’s Radio 2 show and she talked about that. During the interview she said that she will welcome the next Doctor Who companion with open arms when her time is up on the show.
She also said: “I know the time is going to come when Rory and Amy have to leave. It’s inevitable and that will make me really, really sad. But that’ the nature of the show and what’s so good about it. What keeps it exciting is the fact that it’s reinvented all the time with new people. I think that’s a really great part of the show, so I will welcome the new companion with open arms.”
It seems she will return to the show sometime in the future, but it not know (to the public, at least) when. I can only hope it’s as soon as possible. 😀