To save Amy the Doctor sacrifices her unwavering faith in him. Based on recent episodes, the audience can agree that Amy needs to check her faith in the Doctor. He doesn't always come through; he left her waiting as a kid, again on Apalapucia, and forced her to resign herself to the idea of a life without her daughter. The guilt of his experiences with past companions ways heavily on him, thus he decides for Amy that she must stop waiting and make her own "bigger, scarier adventure" with Rory and the house the Doctor gives them, a parting gift for the dozens of close calls (in Rory's case, actual death) they've experienced while traveling in the TARDIS. As a big fan of the Ponds, their departure as full-time companions is somewhat softened knowing each actor has said they will have some sort of role in the upcoming season.