I can understand the frustration, but I would probably find a different way to respond to the challenge of a fundamentalist student. Nonetheless, if students are aggressively challenging teachers with fundamentalist, anti-science claims, then teachers need room to respond. The NCSE reports:
The case originated when Corbett, a twenty-year history teacher at Capistrano Valley High School in Mission Viejo, California, was accused by a student, Chad Farnan, of “repeatedly promoting hostility toward Christians in class and advocating ‘irreligion over religion’ in violation of the First Amendment’s establishment clause,” according to the Orange County Register (May 1, 2009). Farnan cited more than twenty offending statements of Corbett’s in his complaint.
The federal Appeals Court ruled in Corbett’s favor:
In broaching controversial issues like religion, teachers must be sensitive to students’ personal beliefs and take care not to abuse their positions of authority. … But teachers must also be given leeway to challenge students to foster critical thinking skills and develop their analytical abilities. This balance is hard to achieve, and we must be careful not to curb intellectual freedom by imposing dogmatic restrictions that chill teachers from adopting the pedagogical methods they believe are most effective. … At some point a teacher’s comments on religion might cross the line and rise to the level of unconstitutional hostility. But without any cases illuminating the “‘dimly perceive[d] . . . line[ ] of demarcation’” between permissible and impermissible discussion of religion in a college level history class [Corbett was teaching Advanced Placement European history], we cannot conclude that a reasonable teacher standing in Corbett’s shoes would have been on notice that his actions might be unconstitutional.