There are philosophical naturalists, yes. They're a subset of the people who despise creationists.
So, does materialistic naturalistic science reveal it's Godless agenda by
1) sticking to its story despite the evidence or2) revising its story every so often to fit the evidence?
I wish there were no "materialsitic naturalistic" science. I wish there were only "science" that was willing to accept whatever conclusion was allowed by the evidence. Alas, some misdefine science in such a way that certain possible explanations are ruled out in advance regardless of evidence. That is the subjective "materialist naturalistic science" that undermines plain old, non-philosophical, objective science. The kind Newton and Pascal and the rest of the giants practiced.
Now as to the specfics of your question : it does number 2 in the particulars in order to do #1 in the general. In other words, naturalsitic assumptions are NEVER ALLOWED TO BE QUESTIONED! That is "sticking to the story despite the evidence". That is the only story they stick to...that it is all naturalistic. Everything else must be constantly changing to be bent around their one absolute.
That is where #2 comes into play. Any naturalistic explanation, regardless of how contradicted by evidence, is taken to be infinetly better than any supernatural explanation, no matter how obvious. These leads to missing the true explanation so that an infinte series of flase explanations must be tried and discarded, even while the true explanation is sitting there like the elephant in the room.
So I say that they DON'T change regardless of evidence in philosphical underpinnings, and this causes them change constantly in terms of the particulars. Since they miss the obvious truth, that forces them to set a series of untruths as proposed explanations. These are being shot down with increasing rapidity as our power to test hypotheses grows.
I hope I am getting this across. The point is somewhat hard to grasp, how an error on point one of your question leads quite naturally (no divine intervention required!!) to errors of the nature of type two.
1) sticking to its story despite the evidence or
2) revising its story every so often to fit the evidence?"
False Dilemma.
The third option would be they are presenting a story that the evidence does not support. The definitions are constantly being shifted--"evolution" either means "change" or it means "accumulated change to account for biodiversity." There is evidence for the first, and people are supposed to believe that the same evidence accounts for the second. See Hasn't Been Proved
Some of us are not that gulliable.