Alceste, I agree with you that it would be ridiculous to bar teachers from presenting any of their opinions whatsoever in class. It would be prohibitively restrictive and would interfere with their ability to teach effectively.
However, like it or not, freedom of religion is a constitutionally guaranteed right of Americans, and the separation of church and state is an important mechanism for making sure that that right is not infringed upon. As state employees, teachers must honor this separation. Religious opinions, therefore, are necessarily barred from the classroom. They are an exception to the rule that personal opinion has a place in a teacher's repertoire.
Even though only one (strangely chosen) comment by Mr. Corbett was found to cross the line, it does appear that he did have an atmosphere of hostility towards religion in his classroom. "When he (Ishii) signed up for AP Euro in high school, “people were a little concerned -- you’re a Christian,” he remembers them saying to him." If students are warning each other about a particular teacher's religious views, then I think that's troubling. How do you know religious kids didn't avoid taking his class? And even though he promoted open discussion and debate in his class, it can be intimidating to take on the teacher. Debating the teacher just might not be an option for the timid kids.
Unless you want to take on separation of church and state, I just don't see how you can justify blatant religious bias within the classroom.