Since a discussion using the guidelines given to empirical science immediately puts its opposing viewpoint at a disadvantage, a middle ground has to be achieved so that an equal footing can be given to both viewpoints.
The "middle ground" adopted by nearly all believers and unbelievers alike is that when discussing the natural world the methods of science are appropriate for drawing conclusions and for discussion faith, spirituality and feelings about these things then religion is one good source for input.
This is the every popular "non-overlapping magistars" of Gould and many others.
If the methods used in inquiry about the natural world need to be changed I would like a detailed description of how that would work. Given the problem of determining the possibility of life on other planets how would starting from the Bible help?
Given the past history of using the Bible (as an example) as a source to inquire about the natural world wouldn't we be a bit gun shy of such an method. Over and over in history the Bible has been used to support a postition about the natural world and this position has been shown to be unhelpful. Demons cause disease and the Earth as the center of the universe are two examples of this.