"Maybe fond at the time and not in hindsight." She doesn't know the details, but the impression she got is that John's time with him was part of a bad time that he's not proud of.
"Of course you had a choice, just might not've been a choice you'd ever be willing to make. Maybe 'understands' it as far as you'd never choose otherwise." She can't understand herself how this man could still be running loose after that. How do you forgive setting off bombs around Cardiff? There are things her father wasn't telling her, she knows, but that alone should've done it.
Once she realizes what John's implying-- takes a few moments since she'd never think of herself being mistaken for that-- she looks disgusted. "No. It's not like that at all."