The moment she saw his disappointment at this she felt bad. She didn't want him upset, especially when her own body was protesting at the logical side of her. She glanced away, staying on his lap still as she thought. Heart, mind and body were all fighting and for once, Hermione decided on something she probably shouldn't.
"For once," she said softly as she looked at him, "I think I will not listen to logic."
She just had to wait for him to realise that meant she was willing to at least continue kissing. If things became more intense then she would consider her actions then.