This is exactly why we distinguish the natural sciences from the broader spectrum of science (i.e. social science, philosophical science, etc.):
From the Oxford American Dictionary:
natural science
noun (usu. natural sciences)
a branch of science that deals with the physical world, e.g., physics, chemistry, geology, and biology.
the branch of knowledge that deals with the study of the physical world.
DERIVATIVES natural scientist noun
With all due respect, complaining that the natural sciences don't address the supernatural seems to me to be like complaining that a laxative won't get rid of your headache. I'm fine with ID being taught as part of the broader scope of philosophy (as are most other supporters of teaching evolution), but not under the pretense of it being part of the natural science of biology.
Festering laxatives placemark
Methodological naturalism would not apply to science per se - neither indeed would the scientific method.
Also, when you use the phrase natural science of biology you touch on another area of potential healing though the term itself needs to be more specific so that metaphysical naturalism is not presumed, i.e. methodologically natural science of biology.
I can imagine an amusing scene as students gather to learn and do biology. The professor announces this course is on the methodologically natural science of biology. If any of you take this to mean the metaphysically natural science of biology, you are in the wrong room please go to the South wing, and ask for professor Dawkins laboratory, the course name is "atheism 101". If any of you reject methodological naturalism as a presupposition in science, then please proceed to the North wing and ask for professor Behes laboratory, the course name is "intelligent design 101". Whew. Ok, now all of you who remain we will be learning and doing biology with the presumption, not the metaphysics, of naturalism. If any of you try to bring your own ideology or metaphysics to the lab, you will be ejected from the class altogether. LOL!