Great question and great comments.
You started off with "For two thousand years, the ordinary plain text interpretation of the Genesis creation and Noah's was taught by Christians as absolute truth. A seven day creation; the earth is pretty much the center of the universe; Noah's flood was universal; humankind started about 5,000 years ago, near the present day middle east." I just want to correct your misunderstandings. Clement of Alexandria and Origen interpreted Gn. 1 allegorically (as a symbol). Augustine didn't interpret Genesis 1 as literal 7 days, and said the account should not be taken literally (
http://en.wikipedia.org/wiki/Augustine#Creation). The Catholic Church historically believed in creation as a process, and when Darwin published his "On the Origin of the Species," the church affirmed evolution as being compatible with Genesis 1 (
http://en.wikipedia.org/wiki/Catholic_C ... _evolution). It has only been in the past few centuries (The Age of Enlightenment) that some or most Protestant churches took the stance of a literal 7 days. Recently scholars are recognizing the error of that perspective and looking again at Genesis through ancient eyes. I consider it to be rational and a strength to recognize when one is traveling down the wrong road, and to set one's course for a more accurate interpretation. Scientists do it all the time; theologians should be allowed the same course in the pursuit of truth. Archaeology in the past 100 years has brought a world of new information to light, and I, for one, am glad to see Bible scholars responding do it rather than entrenching in beliefs that are increasingly obviously false.
You chide Christian scholars for reacting only when science bombarded culture with knowledge of what really happened. As you know, change in some institutions and disciplines comes with difficulty, and not at all smoothly. The church is infamous for having difficulty with change, but it is happening, and I consider it a good thing. I agree wholeheartedly with you that we are rapidly approaching the day, if we are not there already, when the rejection of evolution will be a thing of the past.
There is no need for anyone defending Biblical accounts to have to desert the text to concur and coexist with geology, astronomy, and evolutionary principles. No defense is necessary. You have erected a false enemy to slay. People are totally mistaken if they think evolutionary theory is incompatible with theistic or Christian belief. The Bible never argues that the earth is only 6,000 years old. A misunderstanding of the genealogies of Gn. 5 led to that misunderstanding, and it's not necessary to interpret the Bible that way. Again referring to Augustine: he didn't believe the world was young. The Bible doesn't require it. The Bible teaches no objection to the claim that life could have progressed from relatively simple to relatively complex forms. The Bible teaches no objection to the idea that the diversity of life has come about by way of offspring differentiation. It also has no problem with the idea that life originated at one place on the earth, and from that all subsequent life has come. The Bible has no inherent qualms about about Darwinism and a naturalistic mechanism driving adaptation and genetic mutation. The only part the Bible would argue against is the idea of scientific materialism—that there is no God, and all there is is matter.
Darwinian evolution talks about mechanisms, selection, and mutations. None of these are contrary to the Scripture or theism. The only mechanism it speculates is random chance. But since the mechanism is unknown by science, then the field of possibilities is open, and just possibly God (as a theist would claim) is that mechanism. Evolutionary science says there is a biological and chemical history to life as we know it, that there is good evidence for the progressions we have seen, and that we know how some of the transitions occurred. There is nothing inherent in those statements to suggest how the process transpired. Neither does the Bible suggest how the process transpired; only that God was part of it. Still no inherent conflict, and no particular further reconciliation necessary. Is it possible, naturally speaking, that unguided natural selection generated what we see today? Of course it's possible. Is it also possible that the process was guided? Of course it is. You may think that the latter view is astronomically improbable, but you've probably seen statistics about the first option also, so we can't go with the argument of "astronomically improbable." There is no reason whatever to think that current biological science is in conflict with Christian belief.
As far as Noah's flood, I don't believe it was universal. You can read my articles on this website about that to get my writing on it. It certainly does not necessitate a conflict with known science.
You seem to be battling the enemy of extremely conservative fundamental Christianity. Please (1) don't put most believers (theists) in that category, and (2) don't think that the Bible HAS to be interpreted that way. It most certainly does not.
I would be pleased to discuss this further with you, getting down to whatever specifics you wish, but hopefully with these clarifications our discussion can be on more established understandings of Scripture and science. As I've said in other places, I believe in good science and I believe in good theology, and all of my understandings of the two see no contradictions and no conflict.