The Church did not “disagree” with him out of fear of science, but instead because they genuinely had no idea whether or not it was scientific fact, because back then a lot of scientific fact that is well known to us could not be proven and was thus perceived as the philosophical opinion of an individual!
I think that’s partly the point. First, the lack of scientific evidence is something retrospective that we attribute to that period. The modern scientific method was somewhat in its infancy at that time, even within scientific circles. As you mentioned, it was taken as philosophy and there was a blurring of boundaries between philosophy and science (and by extension theology as well) for a long time. Most of those in Classical Greek who came up with classical scientific discoveries like Pythagoras etc would have written ‘philosopher’ for Occupation when filling in modern forms. And those whom we see as philosophers today have scientific ideas as well. So, it was probably not like to be accurate to say anyone disagree with anyone else on the basis of absence modern understanding of scientific fact.
Science at that time was more reputational rather evidential - a scientific assertion was true based on who asserted it rather than the modern notion of evidence. The Aristotelian model of the universe endured for a long time despite evidence to the contrary. Even today, much of what we have in nutrition is reputational, slowing being overturned by evidential methods (the idea of 8 pints of water a day was propagated because it was repeated by the authorities when there was no evidence to support it). So, the Aristotelian model was right because it was from Aristotle.
The understanding of the universe by the society at large at that time was Aristotelian and Galileo’s observations upset that model. And the Church did quote Biblical passages (e.g. Ps 104:5) to support the Aristotelian view. At Galileo’s trial at which he was accused of that his assertions was at odds with the Church’s interpretation of the Biblical passages, the arguments by the Church were 18 physical and mathematical arguments, not so much Biblical. The judgement of the court in his first trial was that the heliocentric model was “foolish and absurd in philosophy; and formally heretical since it explicitly contradicts in many places the sense of Holy Scripture”. It was clearly scientific in attempt. It was only in the second trial that the accusation was heresy - “for holding as true the false doctrine taught by some that the sun is the center of the world”. So even his accusation of heresy was based on his science and forbade him to teach his heliocentric model. Of course, with the blurring of science and philosophy (and theology) it is easy to paint Galileo’s heliocentric views as theological as well as scientific. One has to read Church judgements within the context of its times. Also, these were the days of the war with Protestantism before the Peace of Westphalia. In fact, the heliocentric model was said to have tinge of Protestantism.
I would agree with you that the Church did not disagree with Galileo on the basis of science per se. At an immediate level, the Church did have concerns that this was an enroachment over its role to determine theology. From Galileo’s writings and actions it seems unlikely he has any intention to do that - he had no argument with the Church on doctrinal issues and just wanted to get back to his telescope, which he was able to do after his abjuration required by the court. He was threatened with torture if he did not abjure. So the role of the Church in safeguarding theology and doctrines was safe for a while longer, which Galileo never challenged.
In the longer run, however much damage was done to the Church. But it was inevitable whatever the Church did in this case. In the longer run, the Church worried that questioning the Aristotelian model could lead to the questioning of every other received truth from the classical world. And if the static nature of knowledge is threatened, the static nature of Church doctrines cannot be far behind. And they were right: the fall of the Aristotelian model led to the Enlightenment, which led among other things to the secularism of today. So, in that sense the Church was right to be concerned over Galileo.
Today, the Church has apologised over the whole affair, some four centuries later. With hindsight we could all wish the Church could have acted differently, but glossing over the facts does not change the fact that the Church did act incorrectly - by the scientific knowledge, judicial standards, and expectations of the Church’s role of today. At best we can say the Church had the best of intentions but the choices made led to undesired consequences. The Church has probably learnt its lesson on science though the unwarranted reputation of being against science within and without the Church unfortunately remains. Probably the bigger lesson on humility is only slowly being learnt.
(By the Church, I do mean both the decision-makers in the Roman Catholic Church as well as the mass of the faithful)
How do I see the entire Galileo affair? Well, these are all acts of my forefathers in faith. I cannot disavow any of it anymore I can disavow my genetic heritage. Right or wrong this is my history. My Church was never intended to be perfect and correct in all its dealings in the human sphere. There is no reason for any shame on me though, particularly with the passage of so many long centuries. Warts and all, what my forefathers in faith did made me what I am today, warts and all. I can do no more than to embrace my history as to reject it would be to reject my self and my identity. I can only find out all I can from it and learn what I can.
And I invite all Catholics to do the same.
… so when do you want to petition for his Canonization? 
