Being male I can't begin to understand what your wife is experiencing, but it sounds to me like she could do with working somewhere else. There must be other, more forward-thinking companies that would love to hire her.
My thought as well. The problem is this specific workplace. My wife has also experienced the same things that the OP wrote about while a teacher and librarian, two of the most female dominated professions in the country. And this held true even when she has had female bosses.
Well, we're buying an apartment and changing jobs is not an option for both of us. But i'm more worried on a general scale: what if the next place is the same? (which probably is)