In the Moreh he writes that a Malach made the donkey talk. He interprets visions of Malachim as dream state but not the Nisim of Tanach. Where does he negate the ability of a Tzaddik to bring about a miracle? Did he re-interpret Rava bringing rain out of season, or Rebbe Shimon Bar Yochai’s many Nisim when the Gemara called them Nisim?
Truthfully, the fact that he rejects any mention of magic and astrology as a Daas Yachid, when we find quotes from the whole range of Tanain and Amoraim, and never a dissenting voice, makes it sound like an apologetic approach. This is probably why, as you said, it didn’t really last. But it gave a handle to those who can’t accept the straightforward approach, so that they can remain Frum and dismiss these uncomfortable parts as Daas Yachid.