I agree. The problem isn't Islam itself, as the Gnostic-like, more mystical Sufi perspective shows. Even the concept of Islam as submission to God could be interpreted in lots of ways. We can submit to God's will not by being anti-intellectual slaves, but by using what God would have given us, including our cognitive faculties. Early Islam was relatively progressive compared to Christendom.

Still, monotheism itself is liable to hamper intellectual progress even as it stimulates it in certain respects (such as by positing a lawful natural order that can be studied).