Eh, the quote isn't as interesting at it might seem. He's using rationalism in the first quote to mean in contrast to empiricism. There's a debate in classical philosophy over whether one should reason from first principles or rely on empirical observation (with almost everyone largely supporting the first). Some of the people in the late Middle Ages swung too far in the other direction. The important realization is that both are important. One can't get too far without using both.

As to the comment about magic, this shouldn't be surprising. Early natural philosophers were doing the natural thing there, testing hypotheses that looked reasonable to them. They could not have been aware of how much humans naturally construct bad hypotheses involving sympathetic magic and similar issues. Nor for that matter did they know enough about the nature of the universe to appreciate that magic would actually violate basic principles and meta-principles of how the world seems to work. Given what they knew, examining magic and trying to get it to work would be the correct thing to do.