I would have no problem with the Ponds showing up again in the show, but it would need to be done right. What needs to be permanent is that the Doctor never sees them again and that they can't be returned to their own time. But we already know that River will at least see Amy again in order to give her the book she's written.
It might be fun to give them another adventure on their own or where they leave clues for the Doctor to find in order to solve some other mystery...or something. Or maybe an adventure with River and Captain Jack (I still want them to have an episode together).