I don't know about this. I grew up in a time were all kids were still nonchalantly using 'gay' or 'retarded' (sorry for using that term, but I'm only using it as an example) as insults without questioning it. Not just kids either of course, you'd see it everywhere online. I feel like that has definitely lessened. And yes, Mary Sue is used often, but as much as it is ingrained in certain segments of nerd culture, the term is also increasingly reviled in other segments of nerd culture.
At this point, it's taken over by people using it as an 'argument' against any female lead so much that it has lost all meaning in my eyes. Yes, I agree that there are stories where the lead character (the gender doesn't matter) is little more than a unbelievably powerful person who can do no wrong and you should be able to discuss that, but I think using the term 'Mary Sue' is very lacking for that. It's very much a female name, and given current trends that gives it a very nasty sexist subtext. The term 'Barry Sue' exists, but that's used far less and it was only created in the first place as a reaction to the sexist misuse of the 'Mary Sue' term. And it still recalls how the original term was obviously female, which carries a meaning that's just way too uncomfortable.
At this point, I just don't think it works as an argument anymore, even if it's used by sensible, well-intentioned people. SJW also started out as a more jokey, self-deprecating term until it was co-opted by jackasses and is now almost exclusively used by idiots.
Like I said, I think the comparison to Gamergate is apt. For way too long people tried using it as a 'legitimate' criticism about 'fairness in game journalism' before people finally realized what bullshit that was.
I think everyone would be better off avoiding the term altogether. Even if it had any value before (and I heavily doubt that), it carries an unmistakable sexist meaning at this point. There are better ways to discuss badly developed main characters without having to go to that well.