Zoo Rabbi and independent thought

I've been wasting way too much time reading the Zoo rabbi's website and why numerous Orthodox Jewish leaders banned his book which attempt to reconcile science and religion. This ban (AKA the Slifkin affair) is almost 3 years old now, which is why I am just reading about it now.

It does give me a lot to think about, mainly about the pros and cons of independent thought. The argument espoused by many traditionalists is that one should feel free to question and argue within hashkafa but one still must accept certain principles as beyond question. Yet what principles must be accepted as such seems to be under constant debate. Belief in G-d? Belief that the Torah was given by G-d? Belief that the Torah's description of creation is literal, and how literal? Belief that Chazal (the Rabbis of antiquity) are infallible in all matters, even matters of science where they were presumably limited by the accepted thinking of their time? Belief that Rabbis who insist that you must believe in the truth of the matters asserted by Chazal, even if they directly contradict the evidence we have today, are more right than the "minority" opinion that Chazal may have been wrong?

Rabbi Feldman writes a well-written article explaining and supporting the ban on Rabbi Slifkin's books and ideology. But his approach is rooted in a mindset of never questioning the wisdom of the ages, which itself is rooted in never questioning the wisdom of the ages. Logically, we end up with an inverted pyramid of thought, as each new idea has to be made consistent with every old one ever accepted by the old wisdom. His article is also criticized by "halachic" laymen here, here and by Rabbi Slifkin here.

It would have been refreshing to hear well-respected Torah scholars who had refused to support the ban speak out against it. But that would violate the "never question the great rabbis" rule that has implicitly driven the whole controversy.