[Rigelian]

There are many examples, I just can't think of most of them at the moment. Copernicus' radical theory that the Sun was the center of the universe instead of the Earth was rejected by proponents of the Catholic Church, amonst other highly religious people of the times. Of course, the Church was not as adamant about burning all who questioned it at the stake as it was centuries prior. And as the Church was wrong about some of the most basic facts about the universe, people making scientific progress would naturally have to question some of the Church's claims (such as the Earth being the center of the universe).

I'd add Giordano Bruno to your list there. He actaully was burned at the stake. Galileo is an interesting case, because he is often used as the archetypal 'scientist against the church' example, and a heroic figure to atheists (like myself). Unfortunately for that simplistic view, Galilieo was a lifelong devout Catholic; he argued, unsuccessfully in his lifetime, that the church should not pronounce on matters of (yet unproven) physical realities. He was worried about the authority and dignity of the church being diminished when the truth was revealed, in time, by careful experimenters like himself.

This is a view that the church eventually came to share, and pronounced only on ethical/moral matters that are not subject to direct proof, characterised as 'God's domain'. Recent advances in human reproductive science/cloning etc have become the object of such ethical/moral condemnation, as science moves into what is still regarded as 'God's domain'. In Galileo's time the position of the sun and earth was regarded as unquestioningly within that domain.

An interesting potential 'clash' in the near future could be if a biological basis for homosexuality is proven, the church having pronounced pretty unambiguously on that one!