Clearly there are limits but those should be decided by faculty who understand the concept of academic freedom. It's not a good idea to offer astronomy courses on an Earth-centered solar system or geology courses based on the idea that the Earth is only 6000 years old. Those ideas are just too far out on the fringe. You're unlikely to find any university professors who want to teach such courses.
However, there are lots of other controversies that aren't so easily dismissed. If some of the more enlightened Intelligent Design Creationists want to teach a science course at my university, I would not try to prevent them. Just as I didn't try to prevent Michael Behe and Bill Dembski from speaking on my campus.
I firmly believe that university students are mature enough to handle diverse points of view and I prefer that they hear them in the context of an academic environment rather than in church on Sundays. Even if there were no opposing views allowed in the course,1 the fact that the ideas are "out there" would provoke debate and discussion among the students. Hearing different ideas encourages critical thinking. Censorship does not.
If Ken Miller, Francis Collins, or Simon Conway-Morris want to teach a course on theistic evolution, I'd be happy to support them. It would be fun to start a debate about the conflict between science and religion and let students see both sides of the issue.
The situation is much more complicated in the United States since both Intelligent Design Creationism and Theistic Evolution have religious implications. In fact, teaching these subjects can be seen as promoting religion and public school systems are forbidden to do that by certain interpretations the Constitution of the United States. There are even people who would use the legal system to prevent courses on Intelligent Design or Theistic Evolution at publicly-funded American universities. It seems incredible to me that they would resort to lawyers to block the teaching of certain subjects at a university but there you go. The culture in America is different and my American friends don't see this as censorship.
It's fun to watch while my American colleagues wiggle and squirm over this issue. The latest "problems" are whether you can categorically label intelligent design as religion and not science2 and whether you can criticize it in a science class without seeming to criticize religion.3
Read the discussion (with links) at: Rosenhouse: It’s okay to criticize Intelligent Design in science class, but not okay to teach it as science. Here's what Jerry Coyne says in the opening paragraph ....
Jason Rosenhouse’s new article at EvolutionBlog, about the Hedin affair, “Dubious legal analysis from the Discovery Institute” (DI), is really going to tick off the DIers and advocates of intelligent design (ID), but I think Jason has a good point. And that point is that although it’s illegal (as well as dereliction of duty) to teach intelligent design creationism in public schools and universities, it is okay to criticize it, for you can criticize ID on the grounds of bad science without bashing religion. And I think Jason’s right, especially given the legal rulings so far on what constitutes an incursion of religion into public schools.It's okay to criticize ID as bad science but it's illegal and a dereliction of duty to allow any professors to defend ID and make the case that it's actually good science. My head is spinning.
1. A position I would strongly oppose if the course were offered in my department.
2. I think that much of what Intelligent Design Creationists advocate qualifies as science by my definition of science. It's just bad science.
3. There's a fine line between banning all mention of religion and promoting atheism. It's not clear whether promoting a solely materialist view of the world violates the US Constitution.