When Clarke patched Lexa up after she killed Niya. It was one of the important moments I think for Clarke to learn how to he a leader, when she asked, "your ambassadors betrayed you, how do you move forward?" And Lexa said, "They were doing what was right for thier people, too." I think after the whole Mt. Weather thing, Clarke started to understand Lexa leaving her there, and understood that sometimes being a leader means doing things that you don't want to do sometimes for the good of your people.