I just had a thought. With the pace of the episodes so far, I don't believe the Ponds will be gone after episode five. I'm almost positive they'll be back for 12 and/or 13. I know the next two seem very Pond-focused, and though something major will happen, I just think they're too involved with the Silence not to be there at the end of that story. Considering they were able to hide JLC's early appearance, it's conceivable that the "final scene" for Karen and Arthur hasn't quite been filmed yet.
I forgot where I saw it but some interview asked about Amy and Rory leaving and Moffat's response was like "The Pond's storyline is far from over." Of course within the context of the answer it made it sound like it was going to be a major focal point in these next few episodes. but I wonder...