Believe it or not I don't necessarily disagree with the premise of the article. I've read both Cosmos and Demon Haunted World by Sagan and he does play up the religion holds back science angle a little bit, but it ceratainly wasn't the driving theme of the books.
Having read a lot of science books, the most used example by the science community to illustrate the thwarting of science by religion is the whole Galileo/Inquisition thing. This particular incident along with the Giordano Bruno stake burning for heliocentric views have truth in them, but in reality are much more complicated then the witch hunt they're portrayed to be. Bruno, although he espoused heliocentrism, was not really a science person at all and certainly not anyone that the science community should hold up as an example that his mistreatment was a strike against science progress. His beliefs were a mixture of pseudoscience and Gnosticism.
And for Galileo, he definitely was a victim of the church shutting down his worldview, but not as much for the noble reasons that science historians portray. Galileo...for all his brilliance and contributuons to science...was an arrogant ass. Italy during that time was politically controlled by a few powerful families. Galileo found his way into the political circles of the Medici family. Pope Urban had actually given Galileo permission to write his views on heliocentrism as long as they were portrayed alongside of a geocentric worldview as well. But it was the politics of Italy alongside of the fact that Galileo was a bit of a jerk that led to his demise as much as his worldview. An interesting note is that Bruno and Galileo actually shared an Inquisitor... Saint Robert Bellarmine
But church was no saint (pun intended) in these matters either. They did burn Bruno alive for his views, a reprehensible act even if it wasn't solely for scientific belief. And the church did show Galileo instruments of torture when they brought him in for questioning.
What I find interesting is that the church at that time actually adopted the geocentric perspective from the held teachings of science prior to Copernicus' introduction of a sun centered universe. Thomas Aquinas's interpretations of Aristotle and Ptolemy found its way into the church belief system and set the stage for the confrontation between Galileo and the church centuries later. So for me, I believe that the stories of the church holding back science is dramatically overplayed, but the church isn't totally innocent either. They have certainly been guilty of holding onto beliefs long after they are no longer remotely defendable.