Charlie, You cannot apply the Aggadaic rule to the Torah. It might be uncomfortable for someone like you, who identifies with science. However, the Torah is not a book found in a hole, waiting to be deciphered. The Torah was given to us by Hashem. You connot say that the Bria described in it is a Mashal. The Ri Migash explains when we learn the Pasuk literally and when we understand it as a metaphor. When it is an obvious exaggeration, as in towers in the sky, we don’t take it literally. Otherwise, if it can be understood literally, that is what it means.
Had there been science around 3000 years ago, when the Torah was given, you would have an argument that the description was not meant to be taken literally. Now it’s too late. The Torah was given to be understood, and it was understood a certain way for 3000 years. It’s just too late to come and say that Hashem meant something else, that nobody knew, all these years.
How to reconcile the Torah’s description with science’s findings is up to you. The universe could very well have started out at one spot, something that used to bother atheists, and it might have started with a bang. Perhaps you like Rabbi Kaplan’s explanation of old worlds. There are many reconciliation theories out there. Some are silly and some are clever, but there is one invariable: the Torah. This is what the Creator told us. Hashem took us out of Egypt in a grand way, which proved to us that He rules the world. There, He told us that He created the universe in six days, and that we should keep Shabbos in rememberance of that. My Emuna doesn’t have to wait for a theory that explains a six day creation, my science can.