I'm saying it isn't just "regular" scientific reasoning, it's all scientific reasoning, by definition of the word "science".
If you try to bring God into science, then what you are doing is just not "science" any more -- it's something else.
I'm saying you can give it another name, call it whatever you wish, just don't call it "science", because by definition, science is based on Naturalism.
Of course, that is supposed to mean Methodological Naturalism, not Metaphysical-Ontological-Philosophical (MOP) Naturalism, which seems to be the problem concerning you.
In other words, a scientist should be able to put on his Methodological-Natural hat when he gets to work in the morning, and take it off again at the end of the day.
But you describe a different situation, where organizations seem to be snooping into a scientist's religious practices, to see if they might influence his work products.
I find that hard to believe, am more inclined to suspect an excuse rather than real reason.
After all, people get hired or fired from jobs every day, and one often doesn't know the "real reason" and so may be inclined to "fill in the blanks" with something that sounds plausible.
And if there are lawsuits involved, the organization may agree to settle out of court, providing a strict "non disclosure" agreement is signed.
So yet another level of secrecy gets added to an already murky situation.
The bottom line is, a significant number of working scientists are religious enough to attend church regularly, and a much larger number will admit to believing in God, and I doubt if any feel seriously threatened in terms of job security on account of those things.
But maybe I'm wrong, and if so, then that's a shame.
Google E Forest Mims sometime and you’ll understand my beef regarding the antireligious elitism that dominates much scientific thinking nowadays. I do understand the “in between the lines” reasons that cause some folks to lose their jobs and occaisionally such an one may attempt to use red herrings such as “a personal attack on my religious freedoms” to deflect any scrutiny away from one’s shoddy work product or habits(that got one fired in the first place).