Science vs. anti-science

At present there is strong resistence to applying the scientific method in many "controversies." Most notably we are told that science does not preclude religion. In that debate some advocate a more accommodationist position. Larry Moran dissects that erroneous proposition:

Good, let's discuss. We begin by defining terms. I claim that science is a way of knowing based on rational thought, skepticism, and evidence. I claim that when that way of knowing is applied to religious claims, those claims can be shown to be false or, at the very least, unsupported. Thus, if you are committed to science as a valid way of knowing, it follows that, when you stick to that commitment, the vast majority of religious beliefs are not compatible with science.

In essence, if you consistently apply the scientific method to everything you do or think:

You can't claim to be thinking like a scientist while holding on to beliefs that have been refuted by science.

However, being rational and consistent is the work of the Devil, as it inevitably will unmask religion as nothing more than superstition posing as enlightenment. As such, just like the rest of the anti-science movement, they fear to be exposed as peddlers of nonsense and will fight tooth and nail to prevent that.

Update: Responding to comments at the above post Larry Moran explains his description of the National Center for Science and Education (NCSE) position in this matter. He shows several examples of their site linking to pro-religion articles and observes:

Correct me if I'm wrong but that doesn't sound like a neutral position on accommodationism and it doesn't sound like support for the idea that science and religion may be in conflict. It sounds like accommodationism. 

and

I don't see an official NCSE webpage called "Resources for Atheists." I wonder why?

Update II: The conclusion of the response by Joshua Rosenau is:

NCSE's job is not to adjudicate philosophical disputes, but to provide resources to people in crises over the teaching of evolution, and the site is dedicated to providing the resources needed by activists and by citizens caught in the crossfire. It's useful for people in the field to know about theologies that are friendly to evolution, and it is accurate to say that they exist. And at the end of the day, it works. And that's what science is about.

Mike Dunford chimes in and states:

I can only see two options. You can come up with a scientific test that is compatible with your own determination of what people should actually expect to see based on your own view of what the nuances of their beliefs should be. The results of such a test can even reasonably be used to justify your own personal rejection of that belief. Attempting to apply the results more broadly simply doesn't work - you wind up arguing with what you think should exist, rather than what's actually there. Or you can simply admit, however reluctantly, that there are some beliefs that science cannot investigate, because there is no set of physical findings that is incompatible with those beliefs. I can see that being frustrating, but I'm not sure why it's all that confusing.