It's all very well saying you've seen how a plot is going to end up but after the fact but I'm going to make a prediction here. You don't have to read it. In fact, I've left enough empty lines here so you don't have to read the bottom of the page to see what might be regarded as a potential spoiler by simply figuring it out. I could also have egg on my face if I'm wrong.
I think I've figured out how they’re going to get rid of the Ponds. It's rather easy really. These are the only companions that have been collected along their time-line. It's been hinted that the Doctor will see them as Amy is going to have glasses and otherwise be infirmed. Ergo, they'll die natural deaths and the Doctor will vow not to watch another life-time fade out again. This goes back to the Davis stories where the Doctor says he only has companions for a small part of their own life-times. Maybe he wants to be reminded of his own mortality.