One may always question the sufficiency of the evidence, but the point is that we do not always have eyewitness testimony available to us - in fact, we usually don't have it available to us. Nevertheless, that does not prevent us from applying reason to the circumstantial evidence that does exist. Whether that evidence and reasoning is sufficient is for us to decide individually - heck, OJ found 12 folks who decided that the circumstantial evidence and reasoning in his case wasn't good enough. Whether their decision, or yours, is reasonable to others may be another matter, but nobody can make you believe something you don't want to believe.
Belief in supernatural revelation, specifically the propositions of the Bible, is not a denial of the physical realities of the universe. It is a presupposition, as much as is the naturalism of mainstream science.
Of course, but only one of those presuppositions is a part of science, and hence the other has no place in science class. Somewhere else in the curriculum, perhaps, but the scientific method is predicated on a procedural assumption of naturalism - it does not claim that the natural world is all that exists, merely that the natural world is all that science is equipped to deal with.