Yeah, that final scene was a killer. Poor Daryl. And he really had some great lines in this episode: "This ain't us, man." "I ain't saying that was the wrong thing to do, but this is the right thing to do." I wonder if this will effect his relationship with Rick at all.
I doubt it. Rick changed his mind and Merle was simply...being Merle.
And Daryl knows that second part better than anyone else. No reason to hate Rick for it.