[Content Note: Cissexism]
Dear Joss Whedon,
Some women have a penis and testicles. Implying otherwise, even as a joke, is cissexism. Encouraging people who educate you about that to "unfollow [you]" is defensive assholery.
A hypothetical someone in your position saying "whoops, I'm sorry, that was a stupid joke that I didn't think through because of course trans* people (and intersex people and other women with penis/balls) exist and I just forgot that because of my cis privilege, thank you all for the awareness raising" is basically the lowest bar there is for ally work and you've still managed to miss it. That's a problem.
I understand the urge to be defensive over your privilege. I understand the desire to lash out when it feels like the internet is yelling at you. I also understand that a basic foundation of my feminism is being willing to say "I'm sorry, I screwed up" when I screw up and hurt people.
To be honest, I have grave doubts that you are engaging with feminism and feminists in good faith. I would be lying if I said I don't sometimes feel like you do the bare minimum of ally work and then coast on the ocean of cookies flung your way because the rest of (cis male) Hollywood people are that dreadfully awful such that the slightest amount of effort looks like the second coming of feminist-Jesus.
But I am trying to engage with you in good faith and assume that you do have good motives and do want to undermine kyriarchal systems and be an ally to marginalized people. And so I urge you to drop the flippancy over this issue and make a statement affirming that the "joke" was a bad one and that trans* women (and other women with penis and testicles) exist and that (a) they shouldn't be invisibled, even jokingly, and (b) they deserve their stories told just as much as cis women do.
Because there are a lot of transphobic people out there who wrongfully believe that genitals equal gender, and you have a tremendous amount of power to shape the social narratives they engage with. For you, a famous cis man who famously writes Strong Female Characters, to affirm that women who happen to possess penis and/or balls are still women, that would be a real piece of awareness-raising ally-work you could do. That would be leveraging your privilege to help people more marginalized than you.
Therefore I urge you in all good faith to reconsider how you are responding to this issue.
[Hat-tip to Liss. Also: Awesome Venn Diagram by Kate.]