Chief among the difficulties of writing the history of religion and science is that neither religion nor science quite meant what we think they mean today. When we go to the history books looking for science, we get very selective about what qualifies--e.g. improving astronomical measurements-- and misunderstand what our predecessors thought they knew and/or thought they were doing. The same goes for religion. We tend to treat religious beliefs as exclusively personal, or subjective; we expect them to inspire, but not to dictate the truth about the observable world. So when we discover in the history books people using religious beliefs to do just that, we automatically assume that something either is wrong with the way that they thought about the world or that we have made incredible amounts of progress in the intervening centuries--or, as is often the case, both.
Some of the difficulty one encounters when studying the history of religion and science will be mitigated when we consider that our present use of the term 'nature', derived from natural scientific investigation, has an exclusively physical, non-moral quality. Prior to the 20th century (and especially prior to the 19th century), however, the term 'nature' had both physical and moral connotations.
How so? Someone like Richard Dawkins will insist that the human being, explained within the methodological confines of natural scientific study, can get on quite well without supposing they have a spiritual substance called a soul in addition to material that makes up their body. On the other hand, someone like Aristotle, whose theories still had currency in the 18th century, held that the human being was by nature composed of a material body and rational soul. Having or being a soul, which has or is a body, was a way of saying that the life the human being possesses is not merely an individual possession, not merely something a person can dispense with as they choose. Having or being a soul meant that the human being was always already enmeshed in communal webs of moral significance. That idea had an exceptionally long half-life, and has only very recently fallen out of use. The term 'nature' has ceased to include soul; and, as a consequence, it has also ceased to possess intrinsic moral significance.
The lesson to be garnered here is that early modern and pre-modern thinkers ought not to be faulted for falling to understand the natural world properly (i.e. on modern scientific terms). They may have dealt with the problematic of how to relate moral and physical judgments about the world differently than we do at present, but that does not mean all-important moral questions like, How ought I treat other human beings? cease to be relevant today. Whether or not scientific investigation has made splitting the atom a real possibility for us today says nothing about whether I should set a nuclear device off in the middle of a city. In the same sense, whether or not the acceleration due to gravity near the surface of the earth is 9.8 m/s2 says nothing about whether it is morally acceptable to shove a person off a 40th floor balcony. A balance between moral and physical judgments must still be struck.