At the outset of this question I would like to make it clear that I'm not taking sides on whether we should or should not believe the Rambam's (or others) statements. I am talking about contemporary Orthodox Judaism as whole. It seems to me that there are a number fairly extreme "issues" that general contemporary Orthodoxy has with the Rambam, which include but are not limited to his seeming disdain for all things metaphysical(i.e. segulot, amulets, magic etc.), but at the end of day a large portion of our current halachic reality is based on the Rambam's opinions. My question is how do we deal with this dissonance ? It gives the appearance of "picking and choosing" which is not the Jewish way as far as I know.
TL;DR In those days, the attitude of philosophers was not to intertwine philosophy with obedience to the law. Therefore, there was never a need to disavow the non-philosophical works.
Nowadays, when someone makes a philosophical statement that doesn't fit with the common narrative, he is labeled a heretic and his teachings are banned. In the old days, given the same situation, the works in question were labeled heretical and banned if deemed necessary, while the other works were addressed for what they were.
Why? There was an assumption of decency of character where philosophical ideas did not permeate the writer to the extent that every idea he had was influenced by his philosophy. So his understanding of the laws of Shabbos from the Talmud per say, were not influenced by his understanding of the nature of witchcraft, for example.
What changed? Well, the Rambam while opining the ridiculousness of brief in witchcraft, still never said and therefore the laws concerning witchcraft are null and void. An attitude such as this shows his respect for the Torah and its laws.
In the pre-modern era, it became commonplace for many thinkers to point to things they believed were proven wrong or obviously incorrect, and used that to obviate mitzvos. In many situations that attitude spread even to mitzvos that had nothing to do with the subject at hand. That is why bans on people, rather than particular works, became popular.
We cannot use the standards of the modern era, to ban people, and wonder why those standards weren't used in previous times when attitudes from all camps were different.
I think that the article linked to is rather exaggerated - not so much in its portrayal of the Rambam but more in its description of today's consensus.
While it is undeniable that commonly accepted mystical cliches may have made the Rambam turn green, the extent to which people take these (essentially empty) statements is severely exaggerated. Most of us are rationalists even if we may deny it - when we are ill we go to the doctor (rather than just davening or getting a brocho), we don't pay any attention to astrology and we don't just rely on Hashem to feed us. Most of those who go in pilgrimages to Meron and such like do it for the experience and not because they genuinely think that this is an expression of Avodas Hashem.
If anything, it is in halacha that we follow the Rambam least.