Yeah, I have no sympathy for them. The MRA brigade will completely swarm a thread where there's even a hint that the topic might promote women's rights and derail the original topic completely. It's one thing if it was a civil (if passionate) discussion about balancing rights between genders but that's not how the MRA crowd handle it. I don't even have a problem with them behaving that way in their own space (and they have several subs dedicated to the topic), but they raid other subs whenever they see the flag go up.
/r/science has a very targeted mission which they're very explicit about. Derailing it with drama is simply not something they should have to put up with regardless of free speech issues. If you want unrestrained free speech there's always voat, but according to the admins here people who show up just to try to troll for reactions are not going to be welcome.
It's tough to identify the line between free speech and trolling. What the MRA brigade does is not promote free speech, they're trying to shout down anyone who disagrees with them. I have absolutely no problem with what the article says she's been doing to keep that under control.