I have read this book and there are quite a few historical inaccuracies because he reads history thorought the eyes of Andrew White and William Draper's outdated conflict thesis. The White-Draper conflict thesis was discredited in the last century thanks to availability of primary sources and records. For a good review on the myths and inaccuracies found in books like Russell's and other like him, along with clarifications of the situations by many historians of science, please read : Galileo Goes to Jail and Other Myths about Science and Religion. Check out When Science and Christianity Meet which has has numerous historians of science debunking myths found in books like this.
Fortunately, some more up to date academic resources which show the complex relationship between science and religion from diverse perspectives that are more balanced and empirical. Some can be found here :
Science and Religion, 400 B.C. to A.D. 1550: From Aristotle to Copernicus
The Beginnings of Western Science: The European Scientific Tradition in Philosophical, Religious, and Institutional Context, Prehistory to A.D. 1450
Science and Religion: A Historical Introduction (many good entries by multiple researchers)
The Popes and Science, the History of the Papal Relations to Science During the Middle Ages, and Down to Our Own Time (Classic Reprint) (shows how the catholic church and especially Popes supported science and sponsored it more than any other institution in the past)
The Rise of Early Modern Science: Islam, China and the West
Inventing the Flat Earth: Columbus and Modern Historians (a thorough refutation of the Flat Earth Mythology)
Science and Technology in Medieval European Life (The Greenwood Press Daily Life Through History Series: Science and Technology in Everyday Life)
Cathedral, Forge and Waterwheel: Technology and Invention in the Middle Ages
1001 Inventions: The Enduring Legacy of Muslim Civilization
A Sourcebook in Medieval Science (Source Books in the History of the Sciences) (very important anthology since medieval scientists own writings can be found here and many of the "conflict thesis" myths are easily debunked)
It is because of the advances in science in the medieval period that gave rise to modern science of course. It did not emerge in a vaccum.
Also since you mentioned having your beliefs torn, I'll add one more reference for others who want to look into atheism in the history of science. Summary of when modern atheism spawned (17th century, not before), and the relationship it had with science up to this century one can see Oxford and Cambridge's review from the "Investigating Atheism" project under the "Atheism & Science" section online for free. Of course, Big Bang denialism, Mendelian genetics denialism, and other conflicts that atheists have had with science are just a samples from the history of atheism and science (Soviets and the Chinese had quite a few anti-scientific campaigns because some scientific ideas contradicted their worldviews.) Conflicts and peace with science cut both ways.