Does anyone else think it was cruel of Director Shepard to let Tony get close to Jeanne even though she knew they could never be together?

In a way, yes. But at the same time, Tony knew what he was getting himself into when he took the assignment, and I don't think he expected to actually fall in amor with her, and I don't think Jenny expected him to either. As much as I loved Jenny as a character, she did involve the team in her personal vendettas, which was not an ideal thing for a director to do. I think the mission became bigger than either party expected, which doesn't make it okay, but it makes it mais understandable.