and they were right to do so. Galileo was maintaining as fact what he didn't have scientific proof for; he was being an bellybutton about it, engaging in polemic for no particular reason. And, as things turned out, Galileo was wrong too.
Hell, outside of the heliocentric universe (with perfect circular motion, wrong on both counts), the things Galileo was brought up on heresy charges for were common knowledge: sunspots? Alleging the sun and planets had "imperfections"? Medieval scholars discuss those details long before Galileo.
Besides, Holy Inquisition or not, that is a determination of Men against Men, not "The Church". abstract concepts do not act in history, people do. Declarations of ideas heretical do come out from time to time -- even on this board you see those mechanics at work -- but that's really beside the point.
The problem is this:
Intelligent Design is a dumb idea. I mean, stupid dumb. What makes it stupid dumb is not the notion that God can intervene at any point, and that no scientific theory can stand against God's will -- that's not a problem. In fact, if you want to deny absolutely the authority of scientific knowledge in this world, go ahead. What makes it idiotic is that it pretends that scientific knowledge must incorporate the assumptions of faith. Scientific knowledge has nothing to do with revealed truth. And if revealed truth and scientific knowledge clash, there's nothing to prevent any believer from rejecting scientific knowledge outright: that's the clause to Ockham's razor that's often forgotten. For while the claim goes:
entia non sunt multiplicanda praeter necessitatem (beings should not be multiplied beyond necessity, that is, "don't posit more things than are necessary to explain the phenomenon"), Ockham, being a good theologian (and incidentally, a Heretic, but that didn't stop other theologians from studying or building on his work), is quick to add: exceptis divinis ("except in divine matters").
God can do whatever he wants, including subvert the entire order of scientific knowledge.
But an equally dumb idea is that science necessarily excludes religion. One does not rule out the other. People do not believe that the sky is blue in the same way that they believe God exists.
So our late-nineteenth century friends set up "the great battle between science and religion". And they stacked the deck. They needed a time "when the church ruled everything", so they picked the Middle Ages. Never mind that "The Church" was never monolithic, and in the Middle Ages the Church never had unquestioned or absolute authority. Where the facts were lacking, these "Scientists" manufactured them. That's where the "Flat Earth" story comes from; and that's where much of the Galileo stories come from (well, a lot of that is Bertholt Brecht, a good communist playwright, but hardly an historian).
Anyway, I'd recommend reading The Trial of Galileo and Inventing the Flat Earth. Fun stuff.