Men might refer to each other using just their surnames, but I don't know if there were any situations where it was appropriate for a woman to use that form of address for a man. If there were, I suspect it would be only when a close relationship was present, but I'm not sure even that would make it acceptable. Thus, Emma makes no comment whatsoever on Mr. Elton referring to Mr. Knightly as just "Knightly," but it's obnoxious of Mrs. Elton to call him that.
I don't know that Mr. Darcy switching to "Miss Bennet" was a form of respect. I think that was just what anyone would have called Elizabeth Bennet when speaking directly to her without Jane present, and, as you said, how people would talk about her when she was the eldest Miss Bennet in the area/in their acquaintance. He clearly started thinking of her as just Elizabeth at some point, since right after she accepts his proposal at the end of the book, that's what he starts calling her.