I don't really know enough about Islam (other than the basics) and it's dealings with science to discuss it in depth. So you'll have to forgive that my argument comes from a Christian centered base.
Please do me a favour and read this:
http://www.amazon.com/Lost-History-Enduring-Scientists-Thinkers/dp/1426200927
Not the most accurate but the closest in English that I've read
some parts in the book he mentions in Islamic history how religious men stood against Muslim scientists then rulers (Caliphs) had to choose a side, sometimes narrow minded religious people were oppressed and sometimes scientists were sent away, mostly to Baghdad the world's center of knowledge back then. But those are exceptional cases, most of the time scientists were very supported by society and religion, I admit in all religions you'll find narrow minded ones who are against anything new but those don't speak for it they only speak for themselves.
And it shows the tolerance in Islam that all religions lived among them and one time a prime minister (the 2nd man in the country) was Jewish.
My favourite part is Islam in Andalusia and Abu Al-Qasim Al-Zahrawi (Abulcasis), the greatest surgeon of his time if not all time, and a lot of our medical knowledge today is based on his books.
Shows science and religion getting along very well.