Wisdom of the Greeks is disparaged in the Gemara. One fellow asked R. Ishmael when to learn it [after he had already gone through the whole Torah.] Answer: when it is neither day nor night as it says "You shall think in the Law day and night."
So for Ibn Pakuda and the Rambam to hold that learning Physics and Metaphysics is important and even a part of Torah, it takes a jump of faith in the Rishonim [mediaeval authors].
Otherwise looking at the face value definition of "wisdom of the Greeks" would seem to refer to these very same subjects.
But I must add here that it has never been a problem for me to go with the rishonim [mediaeval authors] even when they seem to differ from the simple explanation of the Gemara.
[I was thinking to show why the Rishonim diverge from the simple explanation of the Gemara. But first I would like to say that it is best to have simple faith. After having faith, it is good to have support for faith. Reasons are also good for understanding in what direction you want your faith to follow. After all one has control over what he believes to some degree. After all you can not believe that you can skip and jump to the moon. But there are many other cases where you can rationally choose your beliefs.[when evidence is not conclusive and you can choose where the weight of the evidence goes.]
Ibn Pakuda and other rishonim hold Physics and Metaphysics are part of Torah. Why? Because they explain the "Work of the Divine Chariot and the Work of Creation" as referring to these two subjects.
(The "Work of the Divine Chariot and the Work of Creation" are called "great things" and "the discussions of Abyee and Rava" are called small things. [R. Yochanan ben Zakai was praised for knowing these things ])
