It's the scientism that creates the conflict (along with perhaps a dash of opportunism on the part of some religious folk). Naturalism is much more that simply positing "the uniformity of natural causes." Most Christians who do science accept that as the fundamental faith statement that makes science possible. But the presupposition of naturalism, once accepted, tend to lead the investigator to insist that the discovered results cannot point to a supernatural creator, as if this would spell the end of "science". This changes the whole nature of the discipline from that "before 1859". (Obviously, I believe that good science leads toward the identity of the Creator.)
BTW your post #203 makes your position a lot clearer.
It seems we only disagree on the definition of words. What you call naturalism I would refer to as scientific materialism, which is a religion in its own rite. I concur that there needs to be more open discussion between science and religion; if there was I think some great schisms in public opinion could be bridged (with the usual exception, of course, of the excessively radical fringes on both ends). As Einstein pointed out (much more eloquently than I), science and religion are indispensible to one another. I just think we're all better served if we remember the limitations of each.