Again, the scientific method isn't the same as science. It's a method, that much is clear. If science doesn't find an answer to a question, it doesn't violate the field to substitute the unknown with whatever you want. Granted believing in a deity doesn't abide by the scientific method, it still doesn't make it incompatible with science. For a long time people used to thing the atom was the smallest unit of matter, then came the electron, neutron, and proton. And then quarks. And then there was a point in chemistry in which people assumed an atom was real but had no proof (or technology) to determine that notion. What makes their leap of faith in atoms any different from anyone else's faith?