This pretty much confirms that she was flirting when she said “Sei-san is actually a rapist? Oh no~~ Whatever should I do~~”. The look in her eyes combined with the fact that she specifically addressed “rapist” without mentioning “robber” was a fairly big clue already. I’m pretty sure MC just didn’t notice because he assumed a “pure and innocent country noble” like her would be as ignorant about sex as she was about travel smarts.