The Ponds leaving at the end of The Girl Who Waited is just the perfect end for them. I can see why they'd have the cameo in Closing Time (so they'd still be listed in the Radio Times and therefore their effective departure in the previous episode would be a more successful surprise) and they sort of still had to be in TWORS albeit as a mix of reprising the openener, and alternate versions of themselves, but...
Bringing them back for series 7 was totally unnecessary and undermined it all.
It was The God Complex where they left, actually. But yeah, I agree in full, that was the best way to leave them. They're done with their TARDIS travels and are living happily ever after. Instead, in the end they're left stranded in the past to live out the rest of their lives, which we know they have since we saw their grave saying they lived into their 80s. Worse, there are probably a dozen ways the Doctor could have saved them but didn't with no reason given.
He lives soooo long. He has to know and accept that his companions don't.
Except the Ponds were far more than his normal companions. They were his family. By the end of it, Amy and Rory had pretty much become his adopted parents (age differences notwithstanding), and then they were ripped out of his life. I thought his angst was perfectly justified in this instance.
True, they really were his in-laws. I can understand going into the kind of depression he did after losing them.