Hi, Daniel.
I have not read the Gilson article carefully, so I will restrict my comments to answering your historical question.
The term “methodological naturalism” (a term which neither scientists, nor philosophers of science, nor theologians, used before 1986, which might make us wonder about how necessary it is for religion/science discussions) seems to have two meanings, one narrower, one broader:
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When we are investigating why objects fall, or what causes fever, or what causes the Northern Lights, or how embryos develop in the womb, we don’t use angelic or demonic activity, or the power of wizards or voodoo priests, to explain the causes of these things; we look to “natural” causes, i.e., what we take to be causes resulting from the impersonal laws of nature.
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Science cannot say anything at all, not even by inference, about God, about teleology in nature, etc.
Now, note that everyone – or at least, everyone of significance in the culture-war debates, agrees with #1 (at least regarding how the world works now – some creationists raise objections to this principle when applied to origins, i.e., regarding how the world came to be in its present state).
The disagreement, then, is mainly over #2. Not everyone agrees that we can infer nothing about God, teleology in nature, etc. from scientific work.
Now, in the 17th century, Bacon and Descartes strongly pleaded for removing the discussion of “final causes” (i.e., discussions of purpose or ends in nature) from natural philosophy (the term “natural science” didn’t exist yet). Bacon said that “final cause” belongs in Metaphysics, not Physics (the study of nature broadly). These thinkers seemed to demand #2 above, as well as #1.
I am not aware of many conscious protests against the statements of Descartes and Bacon on this subject. It seems that Bacon and Descartes were articulating a principle which was already beginning to show up in scientific practice, and were pushing for a full, conscious adoption of that principle as the basis of all future science (natural philosophy, physics, whatever name you wish to use). Since science was already starting to go that way, anyway, there probably were not many scientists who wanted to take issue with Bacon and Descartes.
However, the historical situation is much more ambiguous than most modern advocates of #2 above generally admit.
For example, Robert Boyle, founder of modern chemistry, was a strong advocate of focusing on efficient causes rather than final causes; he wanted to study nature as a machine that worked by an internally coherent set of causes, not as something into which God was always sticking a miraculous finger, or in which spirits, angels, etc. were always monkeying about. Hence, it’s not surprising that Boyle liked the clockmaker analogy for nature – nature is runs as mechanically as a clock, not needing outside help to work. Yet even Boyle granted that, if used with caution, notions of final cause or teleology in nature had a place in natural philosophy. In fact, he wrote a whole book (1688) just to define that place: A Disquisition about the Final Causes of Natural Things: Whether, and (if at all) with what Cautions, a Naturalist Should Admit Them? This book, written long after Descartes and Bacon were dead, indicates that Boyle has thought about their view (he mentions Descartes by name), and slightly differs with them about it.
To put his results in short form, and in modern terms, he agrees with the narrow version of MN (#1 above), but not with the wider version of it (#2 above). So when theistic evolutionists and atheists in these debates tell you that modern science has always from the beginning rejected any possibility of inferring anything about God or final causes or teleology in nature from creation, don’t believe them.
In agreement with Boyle, Isaac Newton, in the General Scholium attached to the Principia, says that it is certainly permissible to discourse of God based on his effects in nature, i.e., based on the structure of the cosmos as science has unveiled it.
So it was not an absolute rule of modern science from the beginning that methodological naturalism in sense #2 above had to be accepted.
In the vein of Boyle and Newton, there followed Paley and the 19th century natural theologians of the Bridgewater Treatises. Modern Intelligent Design also operates within that vein. The tradition that science might be able to say something about purpose in nature or an intelligence behind nature has never completely died out.
So it’s not nearly as clear, historically, as modern advocates of MN make out.
