I agree that not explaining a statement like that is cruel, and highly unprofessional. I would not let him just get away with it and would insist to get an explanation.

As for the intrusive thoughts, it depends what kinds. Since you put this in the romantic subforum, I assume the thoughts have that nature? I never had many romantic/sexual thoughts about my Ts but when I did occasionally, I would not fight them and actually just indulge in the fantasies and thought about their meaning. Mine were very clear, explicit transference fantasies and did not show anything I had not known already. They did not hurt anyone and typically came and dissipated quickly. Negative/disturbing/painful thoughts would be a very different issue.