While browsing through issues of Ascent Magazine, an academic Islamic magazine, I wondered if anything like an academic journal studying both the need for and the possibilities for the secularization of the Islamic world existed. I only know of the Institute for the Secularization of Islamic Society, which is not really academic but has some good articles anyway:
http://www.centerforinquiry.net/isis/Basically as ex-Muslims our demand is very simple -- separate religion and state. You can be an ultraconservative traditional Muslim if you want, but there must not be a state religion, nor any legal constraints that prevent non-Muslims or secularists from proposing laws that contradict the Shariah.
Here is Ascent Magazine, btw:
http://www.ascent-magazine.org/It's quite a well-made journal, and I feel there should be a strong counter-response to religious apologia like this. But it would require a lot of hard work, professionalism and some serious scholarship.