And none of the men would even say “Good Shabbos” to her.
I would never say “good shabbos” to a woman in shul whom I didn’t know on a personal level, although I often will when passing in the street.
This is not odd. I say hello to everyone I pass on the street, while I only greet people I know when in the supermarket.
I suppose if I knew a woman was expecting to be greeted I might throw her a “good shabbos”.
I think that if your wife was insulted, it is because she does not have an understanding of the societal norms in yeshivish shuls. Even if you disagree with the practices of society, you must realize that you cannot be insulted when people act based on them. (unless they are insulting in their nature; for example a black person in the Jim Crow South.)