I'm not so sure about this rumor that the Doctor becomes less emotional because of the nanogenes. That doesn't seem to fit the idea of him mourning, which strikes me for the reason his character is going to change. He's been a big kid with the Ponds since he arrived, and when they go, it's going to be like losing his parents in some way.
I think the thematic emphasis needs to be on "memory," as time goes on, specifically that, as Trenzalore comes and the question is asked "Doctor WHO?" will anybody remember him at all. I think that's the real issue at stake, and it's a mistake the Silents have made. They wanted to kill him to keep the question from being asked - well, what if that's the reason the asking of the question is such an issue? The problem in the future isn't that he must say his name - rather it's that nobody will remember the Doctor, because they all think he's dead, or, in the case of the Daleks, they don't remember him at all. What if the problem is also the reverse of the case in TWORS - in that, River wanted the Doctor to know that he was loved and remembered and sent a message that he needs help, and the universe said "Yes." Well now, thanks to those very events, they think he's dead (or don't even know he existed), so there's nobody to help when he needs it himself.