In the scene that they cut and showed in the Confidential, the Doctor said that was their future in this time stream. Since a big theme this season has been all about how time can be rewritten and is not set in stone, I have a feeling that won't really be their future.As for future Rory and Amy...well that can't just be scenery, there must be a point to it.
And since both Matt Smith and Karen Gillan (but not Arthur Darvill) have been signed for next season, I have a feeling that Amy's loss of Rory in "Amy's Choice" was just a warm-up for the real thing.