This is wonderful. Sherlock's reaction to his...mistake felt so very in character, as did his rather garbled attempts to explain things to John. I love the way you describe their growing awareness of a shift in their relationship, as well as the dialogue when they finally get around to talking about everything.

"Sherlock?” John finally broke the silence. That one word captured all he wanted to say. You weren’t there, are you angry, do you want me to leave, how can I leave you, are we ruined forever, why have you been hiding, do you not want me anymore? Somehow two small syllables encapsulated all that worry and confusion and fear, and he knew that Sherlock understood.

I loved that bit rather a lot, I could feel exactly what John was feeling. Also seconding the bit irisbleufic mentioned above, it's quite perfect.