The Real Rambam
While a cursory skimming of the Moreh may give this impression, the Rambam himself writes in the introduction that the Moreh is not intended to be read this way. It is written to be absorbed, piece by piece, sequentially. Reading it this way, there is no doubt that the Moreh gives a disturbing view of Jewish thought 800 years ago, in the same way that Mishneh Torah gives a view, clearly following classical Jewish sources, on halacha. The analysis shows that the halacha is still halacha today, but much of the Jewish thought does not conform to modern "mystical approach" Judaism (hence, it is "disturbing"). The Rambam obviously has SOME mystical approach, as he discusses halachas that were not applicable, even in his time, but it is not the SAME "mystical approach" that is trumpeted today throughout the Charedi world. YET his principles and likely sources conform with classical Judaism in every way.
For instance, the treatise on Hashacha Protis is often displayed as heretical, against what is taught today. The Rambam holds that the events affecting humans are governed by hashgacha protis, while the events governing lower creatures are not. It is well known, that the Ba'al Shem Tov stated (no one is sure on which page of which book, of which tradition) that if a leaf falls and is blown by the wind, it is by hashgacha Protis. Thus, the Rambam has violated a maxim of a mystic and is thereby heretical. However, upon careful examination, one finds that the Baal Shem Tov and the Rambam are in perfect accord. The continuation of the quote from the Besht is that if a leaf falls and is blown by the wind, it is by hashgacha protis, that the viewer may learn from it regarding service to Hashem. No heresy required.
Another good example is the Rambam's defense of the concept that the universe began, as opposed to its being eternal (Moreh II,25). Summary: If we were forced by science to say that the universe was eternal, we could re-examine and reinterpret the verses of the Torah to accept that view. Just as G-d is described as having body parts, and we reject that notion that G-d has a literal body out of necessity and logic, we could also reject the temporality of the universe, if necessary. However, concludes the Rambam, since an equally tenable case can be made for the literal temporality of the universe, we should defend it. (An apparent premise runs under this, in that he must mantain that, as science changes, our hashkafa could change. This presents no problem for him.) He mentions the Muhamedan philosophers that have already, in his time, allegorized the creation, and he dismisses them. In other words, if there is a logical reason to allegorize a principle in Chumash, the Rambam feels we "must and can" do so. However, without such a reason, we should understand literally, even if both cases are equal. While far from the modernist tendency to allegorize everything, it is also far from the fundamentalist extremist tendency to say that scientific observation means nothing. The rejection of dinosaurs for instance is hard to defend in the face of actual physical evidence. The Rambam does not seem to have favored the Fossean approach so popular today ("G-d made this evidence as a test").
Another thing that the casual reader misses in the Moreh is that the Rambam never uses a secular source as the only source for a piece of information. He correlates the secular books that he quotes with the work of the Chachamim, apologetics perhaps, but nowhere near heresy, quite the contrary.
So why the fuss? In a word: Darwin! The emotional repulsion that the modern fundamentalists feel toward what they perceive as Darwinism, akin to diabolical designs, drives them to reject anything, ANYTHING, that might support the notion that we can accept Darwinism into frumkeit. Hence, we must solidify science back at a time before Darwin (or Copernicus, Galileo, Pasteur, in the process), we must assign some fuzzy mystical value to it to prevent critical analysis, and then we must fight fight fight or risk simian ancestry. The Rambam disturbingly rejects giving mystical value to scientific principles, thus undermining this whole mantra defense against Darwin. Note: by "Darwin" in this sense, we mean the Charedi version of satanized Darwin, not the actual theories of the actual scientist of the same name.
Actual Darwin (a somewhat religious Catholic himself) proposed a unique device in that he saw evolving species and diversification as a result of random mutation and natural selection, the survival of the fittest. There is nothing inherently antiTorah about this. It is a discussion of the mechanism of the observed world. But it runs against the grain of "mystical approach" hashgacha where everything is miraculous all the time. Darwinism does not refute that underpinning, just the obviousness of it. And in Charedism all miracles, which occur all day every day, must be the obvious and only explanation. (In fact, that seems to be the prevailing view on how to live in the world with other people as well.) Darwinism is also weak in that diversification, Darwinism's main distinction, seems not to be a matter of time and mutation, but of opportunism. I am sure Darwin would agree that much of his theory would need to be revised in light of modern paleontology. However, anything that smacks of allowing anything Darwinian to filter in, even patently obvious and observal effects, might "confuse" the masses. Rather than reducing the entire matter to a time problem and addressing the question, its seems that many Jewish "authorities" (self appointed though they are) would like to simply declare the king's priviledge. I think that it is blaringly, unavoidably obvious that the Rambam would not have approached the subject in this manner.
This is the root of every "Torah v. Science" conflict. The problem is neither Torah nor science. It is that we have tried to apply an outdated educational apologetic method, a method that was fine for the majority frum, less educated, less scientifically aware Jews of the last few centuries, but is sadly insufficient for our times. We can't blame that on the Rambam.