If science really is permanently committed to methodological naturalism – the philosophical position that restricts all explanations in science to naturalistic explanations - it follows that the aim of science is not generating true theories. Instead, the aim of science would be something like: generating the best theories that can be formulated subject to the restriction that the theories are naturalistic. More and more evidence could come in suggesting that a supernatural being exists, but scientific theories wouldn’t be allowed to acknowledge that possibility.
- Bradley Monton, author of Seeking God in Science: An Atheist Defends Intelligent Design (quote found here)
I'm more inclined to think that the reason scientific theories don't acknowledge God's existence is that God is not part of the natural world. Science studies the creation; theology studies the Creator. I'm discovering that I lean more and more towards an instrumentalist (not sure if I'm quite a social constructivist) view of science. The purpose of science is to understand and explain the world in particular kinds of terms - "natural" ones - so that we can do our best to control nature, or at least to improve our experience in this world. I do still believe in truth - ultimately, there is one true understanding/explanation of nature - I just doubt humanity's ability to find it, and to know that we've found it.
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Science is committed to scientific-type explanations (call that methodological naturalism if you like) because it can't turn a negative scientific finding (e.g. "as yet, I have no explanation of planetary motion") into a positive explanation out of another discipline (e.g. "planets are moved by angels"). There's also what Kuyper called sphere sovereignty, a sensible response to human failings.
That's not to say the possibility of a creator can't be addressed by scientific methods (or scientifically-informed philosophical methods). One might draw certain conclusions if one could discover Garden of Eden states, having no possible prior state according to the laws of physics. One might be able to put lower bounds on the intelligence (or at least computational power) of a hypothetical Designer, by taking an information-theoretic approach. So far, nothing fruitful seems to have come from that line of reasoning (other than the flippant remark that God really likes beetles). In my view, ID has failed to follow this path (or at least failed to do so scientifically) by not producing a suitable quantifiable definition of "complexity."
It is true that there ought to be a unified field of knowledge, but (as you suggest) short of Heaven that seems unlikely. Even unifying different fields of science is a little tricky. Not to mention the unreasonable effectiveness of mathematics in the natural sciences.
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