Anyway, that is not intended as an argument in favor of religious belief today. But it's worth asking whether any rational justification could have been given in the 13th century for a belief in the deep underlying unity of the universe, before we had available the fruits of the research based on that assumption. I think it would have been far more sensible in those days to believe that the universe is just a complicated place with a lot of different kinds of stuff in it, and a lot of different kinds of principle governing what happens to that stuff.
Interestingly, this sort of pluralistic conception of reality is coming back into fashion in some circles, under the heading of the "dappled universe". Nancy Cartwright's work on these topics is really interesting. (FTR: She is trained as a physicist and has no religious agenda.) It's actually shocking how little reason there is to believe in a single set of underlying natural laws when you consider these issues with an open mind.
edit: There's a good (somewhat critical) review of one of Cartwright's book's here [doc]: http://personal.lse.ac.uk/CARTWRIG/PDF%20various/Book%20revi...