I think it really sank in for her when the Doctor was giving his grand speech to the Master. She was listening. She wanted to stand with him, to be by his side. But I don't think it was one defining moment. It was a series of small ones.

Remembering the names of all the people she'd killed.

Helping Nardole, going to Mars to save the Doctor and Bill.

Hearing the music from the 9th legion and the gate keeper defending the world

You could tell that she really hoped she had come far enough for her and the Doctor to be friends again in EATERS OF LIGHT.