This makes me sad and disappointed. Instead of publishing criticism of the operationalisation, the paper is retracted. Why? Because the conclusions weren’t in line with what we as feminists had hoped for. I would have expected a retraction like this from a small journal but not from a Nature outlet. 
For a great overview of the criticism and the reasons why it should not be retracted, listen to this podcast by two doctorate students in psychology:
Sadly, this is how the censorship machine works and the worst part about it is that it can be controlled by third parties having the interest in banning and forbidding certain information (and discussion on it) to be distributed. This is a very effective tool to influence on the overall scientific progress. Just imagine if there would be a huge and important discovery in the future which can change the way we all live, but it will destroy stakeholders’ empires. Of course, they will buy trolls, media attention to make impression this discovery controversial, harmful and fake…
What I found strange about the reaction to this paper was that it could equally well have been read as “Look, people with female mentors seem to have poorer outcomes, this means we still have work to do to increase the effectiveness of female mentors”. Perhaps female mentors try to fight equally hard as male ones for the resources that their grad students and postdocs need, but are held back in that by the patriarchy. I don’t see what’s especially controversial about “We haven’t fixed sexism yet”. Indeed, the people I see most often patting themselves on the back for having fixed sexism are senior faculty, usually male, congratulating themselves on some bureaucratic initiative involving a lot of people saying “sexism is bad, m’kay”.
For what it’s worth I thought the article wasn’t very good — some of the assumptions and measures they used seemed very simplified — but it does look poor when research by two women out of three authors gets called misogynist.
Totally agree with @sTeamTraen on everything you wrote here.