Bingo--I think your point is right on the money here.
Science does not start with an unchallengeable doctrine, it commences instead with careful observation of the natural world, frames a hypothesis that seems to best explain those observations, determines what may be further predicted by that hypothesis, and then goes on to test that hypothesis against further observations (derived, where appropriate, from experimentation). If these further observations do not match the predictions of the hypothesis, then that hypothesis is amended or abandoned as appropriate. This is why the history of science is littered with abandoned hypotheses--but this is part of what doing science means, the errors in science are corrected by its own methodolgy. Dalton's atomic theory was a major step forward in the early 1800's, the best explanation up to that time for the behaviour of matter--but it wasn't the last word by any means, we know vastly more know about the behavior of atomic particles than Dalton ever could, but it was scientists, not churchmen, who built on his work, corrected errors, framed better hypotheses, and tested them. That's how it works: it's called the advancement of knowledge--and we are all beholden to it every time we visit the doctor, or step on board an airplane, or log on to FR, or--well, you get the point :-)
Religion does not (could not/should not) use this methodology. It is pointless (and in some views, blasphemous) to seek naturalistic, scientific 'proof' of God. For many (and I once was one) who feel science threatens faith, then it is a valid option to simply leave science alone and follow your faith. What is not a valid option (in my view, and I'm passionate about this one) is to try and change science to accommodate your faith. This is what I accuse the Creationists of doing. For, if you think TOE is flawed science, then use genuine scientific methodolgy to invalidate the hypothesis; do not break the proven methodolgy of science in order to sneak in wholly unscientific stuff from your existing theological schema! That is dishonest, debasing, and ultimately very dangerous. This is what Stalin did in Russia, the mullahs in Iran, and the Taliban in Afghanistan.
I can think of many, many cases in history where churchmen have persecuted, even to death, scientists for holding religious 'heresies' that are now accepted as everyday commonplaces. I honestly cannot think of a single case in history of a scientist who has persecuted in any degree a religious leader for that leader's scientific views! But I offer this point as a hypothesis: if anyone has a counter-example, I'll revise/abandon my hypothesis here in full accordance with the scientific method!