I think there are plenty of middle eastern scientists and thinkers-- but you don't hear about them because they're all here in the west making careers subsequent to their education in the west. They identify with civilization and its values far more than they do with Islamic law. And most of them are probably Muslim in the same way that I'm Episcopalian; mildly and quietly. It's one of the more unfortunate aspects of life that only the loudest get heard, and mostly the people willing to be loud are radical in one way or another.
Unfortunately, these people had to turn their back on their countries in order to have a future in the modern world. I can sympathize, but it seems to me that the brain drain out of the Islamic world has left behind mostly intelligent thugs (as leaders and terrorists) and untutored peasants. If the middle east is to have a future, they desperately need to retain and regain their intellectual elites, but to do that, the governments and systems of law will have to be fixed first. It's a conundrum.