The relationship between academic freedom and religious institutions has often been disputed. The AAUP, in its 1940 statement, made an exception to academic freedom for religious institutions. However, its 1970 interpretation is more skeptical about the exception, and the AAUP has censured religious institutions for failing to warn faculty about any limits on academic freedom.
Websites:
Statement on Theological and Academic Freedom (7th Day Adventist Church): http://www.adventist.org/beliefs/main_stat36.html
Against Academic Freedom by T.E. Wilder (1994): http://www.visi.com/~contra_m/cm/features/cm11_against.html
Academic Freedom and the Rights of Religious Faculty By John Whitehead President, The Rutherford Institute: http://www.leaderu.com/real/ri-intro/freedom.html
The Idol of Academic Freedom (1993) by James Nuechterlein: http://www.leaderu.com/ftissues/ft9312/articles/nuechterlein.html
Liberating Academic Freedom by George M. Marsden (1998): http://www.leaderu.com/ftissues/ft9812/opinion/marsden.html
When Faced with Opposition (Religious Academic Freedom, interview): http://www.leaderu.com/real/ri9401/oppose.html
A Zion University (BYU, 1997): http://advance.byu.edu/univconf/Bateman97AUC.html
Academic Freedom at Brigham Young (1997 Denver Post): http://www.lds-mormon.com/byu_aaup.shtml
In God We Trust in the Classroom: http://www.cfif.org/htdocs/freedomline/archive/free_line_godwetrust.htm
Patrick Henry College Denied Accredidation Due to Creationism (2002): http://www.christianitytoday.com/ct/2002/118/31.0.html
Catholic Colleges and Academic Freedom (CNN, 2002): http://www.cnn.com/2002/fyi/teachers.ednews/05/28/teaching.catholicism.ap/index.html
Academic Freedom, Creationism, and the Meaning of Democracy, By Massimo Pigliucci (1999): http://www.korrnet.org/reality/rc/1999_summer/academic_freedom.htm
The Issue of Academic Freedom (BYU Magazine, 1997): http://advance.byu.edu/bym/1997/97winter/academicfreedom.html
Academic Freedom and the Catholic University (1997): http://www.stthomas.edu/cathstudies/1997/
Alan Wolfe, The Opening of the Evangelical Mind (October 2000): http://www.theatlantic.com/issues/2000/10/wolfe4.htm
Interview with George Marsden, on religion and academia (October 2000): http://www.theatlantic.com/issues/2000/10/wolfe-marsden.htm
Academic Freedom on Religious Campuses (1999) by James R. Otteson: http://www.fee.org/vnews.php?nid=4404