Scot McKnight wrote an interesting post today on the need for academic freedom in religious schools. First let me note that I agree with the need for academic freedom, and that I am sympathetic with all three cases McKnight mentions, and have had personal correspondence with one of them. In addition, I like to promote discussion that is as broad as possible.
I do want to put a note of my own, however. I think that religious schools should be able to set the boundaries on what they are going to permit. Will some of them set boundaries I would disapprove? Of course. Many already do set boundaries that would exclude me. In a free market of ideas, I would only object if an institution advertised itself falsely, i.e. claimed to have standards of academic freedom which were not true.
In addition, someone who intends to be a researcher at such a school should be aware of such limitations. If you are doing research at an institution that requires your results to fit in with a 6000 year old earth, for example, you must be prepared for a certain amount of disdain from mainstream science.
Academic freedom is important, and if certain results are excluded a priori, one needs to be aware of the fact.