I must admit that I was genuinely surprised by this. I have worked in Astronomy (as a technologist) for over a decade, and I have never witnessed this sort of behaviour. Of course, I am male. There are, however, plenty of assholes in the world including in academia, and I have noticed that universities tend not to want to rock the boat, so I suppose that it is not entirely surprising that these things are occurring.…
Based on your description, it sounds like your wife has experienced a decent amount of harassment. (I include that extreme bullying in it.) When a number of individual assholes are allowed to continue being assholes, and you need to have a "look out for yourself attitude", that is a systemic problem. I'm genuinely curious what your wife's take is - she may see it a little differently from you.
It seems to matter quite a lot to people whether harassment is characterized as gender-based or not, and we don't have any apparent evidence that it is.
Though I've never really been sure why being a jerk to someone because they're a woman should be any different than being a jerk in exactly the same way for some entirely different (yet no doubt equally stupid) reason.