He has always loved her.

I like the idea of Sherlock realising that he loved Molly under duress. I see no issue with the idea at all. It makes perfect sense to me. This is Sherlock Holmes after all. Loving someone romantically has never been an option. He wouldn’t even consider asking himself the question. Add his life-long conviction taught by Mycroft that caring is a disadvantage, the repressed loss of Victor, the loss of Mary, the constant threat of losing John and the case of Irene Adler to the mix and that’s what you get: Being in love? Never. … More He has always loved her.