Yeah, it sounds like one book with one particular section that is a bit inappropriate for children (never read that book, but from the passage quoted it sounds like a description of a sexual assault). Not sure what age range that school is, I could well-imagine having read something like that at 12 and been a bit disturbed, but also confused by the unfamiliar terminology. Heck, I remember reading more than one novel at that age that featured unpleasant violence that made me feel physically unwell (one I think was a novel about colonial Vietnam that involved description of torture). Even "1984" was a bit brutal, as I recall, to read at that age.
Strictly, such books probably shouldn't be in a school library for children of that age (but I think 12 is right on the border of being mature enough to cope with such reading material), but it sounds like an overblown row over just one book not being fully vetted.
I do remember being shocked, at even a younger age than that, by the blatent racism and imperialism in the "Biggles" books!