Generally, I don't believe the academy is as bad as many of my fellow Christians contend. Yes it's bad, but I don't think it's the new Babylon. That said, if these allegations are true, Professor Kauffman should be fired, regardless of his tenure status. And the faculty member[s] on the ethics review panel who asked the student questions such as "Do you think I’m a sinner" should also be punished.
It does reinforce what my experience in academia taught: the department least antagonistic toward believers is the physics department. And if you want rabid, foaming-at-the-mouth anti-theists, the best place to look is in the humanities.