What you mean "we," Kimosabe?
Seriously: What need is there to prescribe how scientists should study Nature?
I assume that some scientists are proponents of "Intelligent Design," while others are not. So, why not let each individual scientist study Nature as he sees fit?
Astrophysicists who prefer to use Ouija boards - rather than established scientific theories - to predict astrophysical phenomena are free to do so.
Geologists who prefer to use "dowsing rods" - rather than logic based on established scientific theories - to find veins of valuable minerals are free to do so.
Chemists who subscribe to the "Phlogiston Theory" - rather than accepting the existence of oxygen - are free to proceed under those assumptions.
Etc., etc.
We'll see who derives the more useful findings.
Regards,
The chance that science will advance mankind to the stars: 100%
The chance that religion will advance us to the stars: 0%