I can appreciate that the involvement of religion with education has had some negative impact on scientific and social development, but I would have thought that overall historically it has probably had a positive effect.

Note that I say this as an atheist and as someone who doesn't think that there is much place for religion in modern education, apart from learning about religions as part of general cultural awareness.

Well, how about the one that preserved knowledge through the dark ages then?

Isn't a lot of modern academic opinion turning against the idea of any kind of significant 'dark age' actually having occurred in Europe?

http://en.wikipedia.org/wiki/Dark_Ages

They seem to be avoiding the term "Dark Age" but there is no doubt that there was a huge collapse in the infrastructure of civil society and technology after the Western Empire ended.

Note that there was also an earlier Bronze Age "Dark Age" in Eastern Europe:

http://en.wikipedia.org/wiki/Bronze_Age_collapse

If it hadn't been for religion, we wouldn't have spent 1000 years in the dark ages.

So the preserved knowledge is only a tiny slither of what they destroyed.