It would seem to me that the way to solve this is to not use religious assumptions in science and to not use scientific assumptions in religion. Even as an atheist, I still use non-scientific assumptions in my relationships with other people, and in parts of my worldview. I also embrace the subjective and emotional nature of those assumptions and understand them for what they are. I think it is entirely human to have subjective and objective pieces within our worldviews since we are both a rational and emotional species.