You're right. I think I pulled that one out after looking at Genesis too much earlier in the thread (which on a literal reading does reflect a flat-earth cosmology). It wasn't really ever a legitimate church position though.
Flat Earth - Wikipedia, the free encyclopedia Firmament - Wikipedia, the free encyclopedia
Um, so was the geocentric theory they were using...
My favorite source (namely Wikipedia) doesn't have much in the way of good citations on this one. The following is from a student article that is friendly to your position.
Does the history of the so-called Copernican Revolution show that science and religion are antithetical and incompatible ways of looking at the world?
I'm going to nitpick a bit, but your original question was which ideas have been rejected and/or corrupted, not seriously repressed. The church now doesn't have sufficient power to "repress" an idea, so I'd agree with you there. Religious thought still rejects and corrupts these things though.
Your characterization of the intelligent design is also very much incorrect. It doesn't "[question] certain obvious flaws which scientists refuse to examine."
Science in general is progressing towards answers where they are available. Instead, intelligent design seizes upon yet unexplained phenomena and then injects a hypothesis of a designer to explain them. The problem is that hypothesis does not produce any useful or testable predictions, cannot be refuted through testing, multiplies entities beyond necessity, and is motivated by preexisting religious biases. These are the hallmarks of a philosophical theory, not a scientific one. I have no problem with discussing it in such a context, it has been around for at least hundreds, if not thousands of years. But, many people are highly motivated to get ID into science classrooms, again due to purely religious considerations. Sounds like the corruption of science to me.
The fact that three entities all have a property doesn't change the fact that one of them has that property. Its just not highly relevant to the issue of religion's impact.