As far as I can remember, Sherlock Holmes has never in the thirteen episodes of Sherlock lost control over anything or anyone. But he lost control over Molly in TFP. ( Benedict’s words) This is not to say that he doesn’t care deeply for others. We saw him risk his life to save John, Mary, Irene and Mycroft. (and I’m sure he wouldn’t hesitate to do the same for Rosie, Mrs. Hudson and Lestrade). But he was always in control. I have never seen him reacts the way he reacted to Molly being in danger before.
“The one person he thought didn’t matter at all to me was the one person who mattered most.”
Even though I’m a hardcore Sherlolly shipper, I always thought Sherlock was talking about his plan here. About how Molly was important for him to carry out his plan. I think I understand what he really meant now. She matters the most.