Can we just take a moment here to talk about this scene. He has mentioned her, as Professor Song to Clara. He has not mentioned her as Professor River Song or as his wife. Because it hurt him too much to be even as specific as her first name.
Clara: Who was she? The lady with the funny name and the space hair?
Doctor: An old…friend, of mine.
Clara: What, like an ex?
Doctor: Yes an ex. River asked Vastra for the exact words, what were they?
Clara: “The Doctor has a secret he will take to the grave, it is discovered—”
Doctor: *crying*
Clara: Doctor…
Doctor: And it was Trenzalore, it was definitely Trenzalore?
Clara: *nods* Yeah.
Doctor: *cries* Sorry. *jumps up and runs out of the house*
This is probably the first time he has said River’s name in a long time, because it is just too hard for him. This man is heartbroken, and instead of wearing his hearts on his sleeve he has decided not to talk about her like she is his wife. Clara doesn’t know who she is so she doesn’t know the significance of her, so she doesn’t understand why he’s crying. But we know, we know who River is and why it would effect him so much.
Even when she follows him into the TARDIS he doesn’t fill Clara in quite yet, he just says. “River would know though. River always knew.” There’s a fondness and sadness in his voice, but there’s no use saying “Professor Song” anymore. Clara has met her. He can’t hide behind River’s title anymore.
When he sees her grave later he has a hard time dealing with that, but he hides it a lot better than before. But the presence of her grave doesn’t make sense to him. He can hear Clara and River. So I’m sure when River said things so that Clara would repeat them, he listened to River. Clara just repeated her.
Also, I don’t know if anyone caught it or not…but…
River: Maybe it’s a secret entrance to the tomb.
Clara: Maybe it’s a secret entrance to the tomb!
Doctor: Right! Makes sense! They’d never bury my wife out here!
Clara: Your WHAT — ?
Doctor: *looks at Clara and gasps*
*they then fall through the ground*
I don’t think he meant to explain who River was, but in the heat of the moment he calls her his wife. He wasn’t doing that to tell Clara, “oh yeah, River’s my wife, but she died, so yeah…” It was a gut reaction. “They’d never bury my wife out here.” I think that’s one book he didn’t want to open to Clara. I don’t think it was that he didn’t trust her with that information, I think it was because he didn’t want to talk about her, because it hurt him too much.
Clara: Where are we?
Doctor: Catacombs.
Clara: I hate catacombs. So how come I met your dead wife?
Doctor: Oh you know how it is when you lose someone close to you. I sort of made a backup.
River: I died saving him. In return he saved me to a database in the biggest library in the universe. Left me like a book on a shelf. Didn’t even say goodbye. He doesn’t like endings.
Can I also point out that The Doctor stops a little ways up. Since he can hear and see River, he is letting her explain it to Clara so that he doesn’t have to. I think it would be too painful for him to have to explain that to Clara, so when River offers up this information he waits for River to explain.
I can only imagine what must have gone through his head though when River said, “left me like a book on a shelf. … He doesn’t like endings.” River knows him better than anyone, and he knows she’s right, but I think a part of him may have crumpled at that, he had hurt her, in an effort to not hurt himself.
He cries for River. There’s no doubt in my mind. He’s done such a good job at not mentioning her, and not dealing with her death because he’s been in denial, but he can’t deny it anymore. And Clara has now seen River, and now in a sense, the book is off the shelf.
