Yes, you are right. "Science" means knowledge, and only took on a more particular meaning, previously denoted by the term "natural philosophy," in the late Renaissance.
Pope Benedict has been pointing out the dangers of splitting rational thought from religion. Ultimately, it is theology and philosophy that lay the groundwork for science, and when scientists casually dismiss this ancient, hard-won knowledge, they are cutting away the very foundations of their work.
I agree. It is a way of thinking that dictates what science is.
This means that even though a particular science restricts itself to particular objects (as betty boop says, "science must confine itself to the elucidation of the physical"), scientific thinking is not neutral with respect to the very position it takes to dictate its method and object.