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". . . The church had a physical theory about the behaviors of two bodies, even if you hold your breath until you turn blue insisting that this can't be called a scientific theory. A label does not determine the nature of a thing. The nature of a thing determines whether a label is accurate or not. If it smells like a theory about how the physical world behaves, and looks like a theory about how the physical world, and you are willing to throw people in jail for contradicting you, than it is a theory about how the physical world behaves--which is close enough to being science for government work--and you, in fact, endorsed it."

The Catholic Church did have a theory about how the physical world worked. It was not rooted in science. It was rooted in Holy Scripture and, in the Catholic Church's eyes, was only supported by the Ptolemaic world-view that placed the earth at the center of the universe. At no time during Galileo's trial did the inquisitors hold up scripture as validating Ptolemy's work. No; it was the other way around, Ptolemy validated scripture, which was primary.

If you want to refer to the theory of the behavior of physical bodies the Church supported as being rooted in the physical observation of the universe placed above the authority of scripture, which would have made the theory the product of "empirical reasoning" (knowledge derived from the inductive method of observing phenomena), then I will argue with you because the Catholic Church clearly placed the authority of scripture above that of empirical observation. The primacy of empirical observation and inductive reasoning is what defines the nature of science as we know it today and the epistomelogical question that was confronted in Galileo's trial went to the very heart of what should be considered "scientific." And it was in the ensuing decades following Galileo's trial that question was settled in a form which is still recognizable to us to this day. Within fifteen years of the conclusion of Galileo's trial a well-formed debate within rationalist philosophy had developed between the Materialists, of whom Thomas Hobbes became their primary spokesman, and the Rationalists, who looked to René Descartes. As far as the question of what should truly be considered "science" went, the argument was settled by Isaac Newton, who developed his strict Scientific Method some fifty to sixty years after Galileo's trial, which is still practiced today.

Now; I notice that you used the term "physical theory" separate from "scientific theory." If you want to argue that, in Galileo's trial, the Catholic Church held up a metaphysical theory of the way physical bodies behave as superior to a scientific theory, as we use the term "scientific" today, then I can agree, because this clearly is what occurred and in that event you may refer to it as a "phyical theory," provided that recognition of its metaphysical epistemological origins is recognized.

To use the terms you have set out, it is the metaphysical origns of the theory of the behavior of physical bodies the Catholic Church confronted Galileo with which defines the "nature of the thing." Not the label "physical theory," which might imply "scientific" in the eyes of many observers.

... the Catholic Church clearly placed the authority of scripture above that of empirical observation. The primacy of empirical observation and inductive reasoning is what defines the nature of science as we know it today and the epistomelogical question that was confronted in Galileo's trial went to the very heart of what should be considered "scientific."

Exactly. Galileo addressed the issue in a letter which ended up being used against him:
Letter to the Grand Duchess Christina of Tuscany. Excerpts:

... I think that in discussions of physical problems we ought to begin not from the authority of scriptural passages but from sense experiences and necessary demonstrations ...
... it appears that nothing physical which sense experience sets before our eyes, or which necessary demonstrations prove to us, ought to be called in question (much less condemned) upon the testimony of biblical passages which may have some different meaning beneath their words.
... I should think it would be the part of prudence not to permit anyone to usurp scriptural texts and force them in some way to maintain any physical conclusion to be true, when at some future time the senses and demonstrative or necessary reasons may show the contrary.

More than 350 years later, the Church adopted Galileo's approach: The Pope's 1996 statement on evolution. Excerpts:

... I had the opportunity, with regard to Galileo, to draw attention to the need of a rigorous hermeneutic for the correct interpretation of the inspired word. It is necessary to determine the proper sense of Scripture, while avoiding any unwarranted interpretations that make it say what it does not intend to say. In order to delineate the field of their own study, the exegete and the theologian must keep informed about the results achieved by the natural sciences.

The Catholic Church did have a theory about how the physical world worked. It was not rooted in science.

How is the theory that there could be other intelligent beings on other planets inadvertantly sending us radio waves "rooted in science"? Does that make SETI a non-science? Was the theory of aether non-science? Is string theory a non-science? All important new scientific ideas are based on inspiration that did not perfectly obviously arise in some plodding methodical manner from physical observation. Why should I consider holy inspiration any different from secular inspiration in that regard? Is the Einsteinian universe a scriptural, rather than scientific explanation simply because it doesn't obviously occur to everyone just from observing Newtonian behavior?

The primary use of the word "metaphysical", by the way, encompasses abstract scientific and/or physical explanations of natural behavior. If you, (I think quite improperly) wish to claim that there is some high wall cleanly insulating religious inspiration from physical or scientific explanation, than "supernatural" is the better word.

So...in other words, the Holy See brought forward physical evidence by way of endorsing their physical theory.

Well, huh.

Let's jest dwell for a moment on part of the Pope's 1996 message:

In order to delineate the field of their own study, the exegete and the theologian must keep informed about the results achieved by the natural sciences.

So it appears to me, that the church does, and did, in fact, think it has/had an, in some manner, scientific theory once opposed to Galileo's, and now in favor (in the sense of not wishing to contradict) Darwin's.