She was glad that he started to relax, though she continued to rub his back in what she hoped was a soothing manner. Hermione could sort of understand where he was coming from and she hoped that she could help him at least work through what he was feeling. At the very least, she could reassure him that he was quite straight.
"I don't think it was anything you did or said, Severus. I think he's simply confused and he thought that his conclusion was the only viable one based on the man he is now. I think that it might be worth telling him a little bit about the history between you," she suggested softly. It wasn't the most ideal, but it would be a step forward for both of them.