That fallacy is a caricature, of course.
With Copernicus, again look at the details. Copernicus got away with the science per se. What got him in trouble was defying church authority about how to phrase it. It didn't help at all that he put the pope's arguments in the mouth of his fool character in the dialogues. The Catholic church has a genuinely bad record about lots of things, but it is, for instance, one of the few to acknowledge plainly and officially today that evolution is genuine science to be taken seriously.
It really is true that a large fraction of the early work in any science was done by religious people, who in a paraphrase of Augustine's words felt that they were "reading that other book written by God: nature". And also true that the idea that the world was governed by a single orderly scheme, which arose strongly in the monotheistic religions, was an important precursor of science. Fools there are, and fools there have always been. Most of the fools are religious whenever and wherever most people are religious. There is a genuine tension between the approaches taken by science and religion, of course, and the competition for loudest modern anti-science fools is between the religious right and the economic interests that urge them on. But the idea that the two must be eternal enemies is a new one and one I don't think is correct.
The names I didn't have with me when writing an earlier post were John William Draper and Andrew Dixon White. They are largely responsible for the impression widely held today that science and religion must always be enemies. That was not a widely held idea before late in late in the 19th century. For this history, see p139 and the following section of Understanding Fundamentailsm and Evangelicalism, by George M Marsden ISBN 978-0-8028-0539-3. The Great Courses videos on "Science and Religion" offer much the same story.
So what is a self-described "non-religious" person doing with all these references? I'm interested in religion as a phenomenon, and being a scientist I'm in the habit of looking at the evidence.