MarkB
Legend
I think it's possible that there had been a longer interval than just two weeks since the cyber attack. We only know that she had called him two weeks before, but I'm also open to the possibility that she's still pregnant and not far along.
The scene where Danny sends the kid back is captioned "Two weeks later", and it doesn't seem like the meeting with the Doctor takes place much after that.
I don't know how else "Danny and I will be fine" makes sense. And the doctor knows, which is why the remark doesn't strike him as odd.
The whole point of that final scene is that Clara and the Doctor are ending their relationship exactly as they were pursuing it - both lying to each other to spare the other's feelings, both so practised at it that it comes naturally and totally convincingly.