Sherlock looks at John like ‘No, you idiot, I wanted to marry you.’
This line comes after Sherlock notes out that Mary befriended Janine in order to get close to Magnussen, and Mary points out that Sherlock did the same. Fake relationships, fake declarations; a fake proposal. John watched Sherlock betray someone who loved him without a second thought, and he’s just aligned Sherlock with Mary, who’s been lying to him since the day they met. He must feel as though nothing with these two is real at this point; Sherlock convinced Janine that it was safe to love him, and John must feel that Mary convinced him of the same. Human error, and he fell into the same trap.
I don’t see “you idiot” in Sherlock’s face there. What I see there is:
I’m sorry. I know you’re in a lot of pain right now and I’m sorry for that, too. There is nothing false about how I feel about you. But how can I expect you to believe that? She lied to you, and so did I. I’m sorry, John. I’m so, so sorry. You don’t deserve this, you really don’t.
Actually I don’t know if I’ve ever seen Sherlock make a face like that. It’s a very tender face, a very contrite face, a deeply concerned face. It’s the facial equivalent to reaching out and squeezing John’s hand. But it’s only there for a few seconds before he puts his work face back on and gets back to it.
This is my opinion too. Like he can’t say it, but that face is full of regret at all the pain he knows he’s caused John. Its as much of an apology as he can manage. Because John’s comment then was a snide remark that put Sherlock as low as Mary, even if John was siding with him. He was still hurt. And it was the kind of wound that might not ever heal completely. And Sherlock knows that.