Problems with Scripture

Tonight I read Genesis 1 to my six year-old at her request and I had to admit to some misgivings. As you know I am the member of an outspoken Presbyterian church which strongly adheres to the concept of a literal understanding of the Genesis story of creation. In other words, my church states that God created the world in six days (seven if you include His day of rest) and that the entire creation is but a few thousand years old. This is a concept that I have believed for most of my life, but I have come to seriously doubt these details in recent years. This, of course, is no less than heresy in the eyes of those with whom I fellowship and share genetic traits. So I feel like defending myself, if only for the sake of seeing how brilliant I am to myself.
In the beginning of my defense I must state that we have made a great deal of certain interpretations of the Bible as "ultra-conservative" Christians. We feel the need to defend our faith against all comers due to the fact that our faith has constantly been under attack by the "ultra-scientific" for more than three centuries. I have had some of my fellow Christians take offense at my belief that dinosaurs were real because these great lizards had been upheld as proof that evolution is true. My foray into questioning the truth of the creation story of Genesis began as the result of my father telling me that he believed in a non-evidence-based theory of health care because it is the most true to Scripture. In other words he tossed out the whole record of scientific inquiry into health care practices because its conclusions seemed to him to disagree with Scripture. Now one could debate his understanding of Scripture, but I am forced to consider the more basic problem raised by this stand. Is there any other area where science must be abandoned because it disagreed with the dogma that has become essential to some religious doctrine? In other words, is it right to throw out the observations of science because they disagree with so-called Scriptural dogma? My father and the pastor of my church say yes. I say no.
Here is the deal. God had the Bible written to guide us into His understanding of life. One can find this in Paul's statement that all Scripture is "profitable for teaching, for reproof, for correction, for training in righteousness; so that the man of God may be adequate, equipped for every good work." (2Tim 3:16-17) This must be acknowledged from the start to understand why the Bible exists at all, and to understand how to approach Scripture. This means that the Genesis story was written for the purposes stated above, and that it cannot be discounted in importance. We must acknowledge that God created the world the way He stated it was created. Now there is a problem. Scientific evidence states unequivocally that the creation is millions, if not billions, of years old. So what do we do with this? What do you think needs to be done with this? Do we toss this out because the rest of Scripture clearly indicates that the time from Day One to now cannot be more than a few thousand years? I want to think about it a little...