I've watched through season (series) 4. I see a clear message that within any kind of official system, when seeking justice within an established framework, June is (and feminists, or people seeking fair treatment for women, are) limited not just by the fact that most of the power players are men, but even more so by the fact that the system relies on structural inequality between men and women (among other inequalities).
Just adding in individual women in positions of power isn't a game changer. Agent Mark Tuello could be replaced with a woman, the Canadian PM could be a woman (hey, Kim Campbell lasted four months!), the international tribunal hearing Fred Waterford's self-defense could be packed with women, and patriarchy and misogyny could still remain unchecked. Look at Scotland or Germany or New Zealand in real life. Gilead is especially and obviously bad because it removes almost all options for any individual women who might thrive in Canada or old-style USA. We see that with Lydia and Serena, who in their pre-Gilead lives did better than the men around them. But those less-bad systems aren't great (fair, equal, equitable, egalitarian) for women either.
Sometimes it even seems like individual women in power positions can make the problem of ingrained misogyny worse, because the societal expectations of women are different from those of men. See the last UK Labour leadership contest, where all of the women candidates for Leader and Deputy Leader were automatically expected to (and did) sign a misogynistic pledge while men like Ian Murray and Richard Burgon were politely invited to discuss the same pledge, and never did sign it (nor did Keir Starmer).
Then again, I've seen no sign that any of the woman candidates resisted, except for the observation that the pledge was defamatory from Emily Thornberry, who signed it anyway and then dropped out of the race. But we see what happens when a woman politician DOES resist that kind of institutional (and social, and cultural) misogyny - see Carmen Calvo, Rosie Duffield, Joanna Cherry, Joan MacAlpine. Who'd volunteer for that treatment? What's been the blowback for Murray, Burgon, Starmer? Not saying there was none - we've seen some severe blowback for men too, like Graham Linehan, and I know David TC Davies was routinely harrassed - but in politics it seems typically less crippling for men than for women.
Sorry, back to THT - in S2, when the Mexican delegation came to Gilead to negotiate to rent their own handmaids, some of the members of the delegation were woman, and one appeared to have sympathy for June specifically - but nothing changed. The misogyny of disregarding woman, of expecting women to be collateral damage, is so ingrained in the culture that it replicates itself, even if it's not actively pushed top-down.
As for Atwood, I wonder how much she was impacted by her own "bad feminist" moment, when she defended Steven Galloway, the Canadian writer and professor and once head of the Creative Writing program at UBC who was accused of sexual harrassment and sexual assault by a student who'd been in a relationship with him for two years (he said consensual relationship, she said grooming and coercion). Atwood's point back then wasn't that Galloway was innocent, just that the case was mishandled (it was dealt with as an internal matter by the university, and Galloway wasn't given certain rights he would have been in a criminal case in a Canadian court, such as knowing in advance what he was accused of doing). She was hounded for it (and I don't mean harsh but fair and reasoned criticism, I mean harrassment and attempted silencing); if anyone's curious, she writes about it here: www.theglobeandmail.com/opinion/am-i-a-bad-feminist/article37591823/
Atwood's comments on JK Rowling were ignorant - whatever you think about erasing the legal distinction between men and women, it should be possible to express those thoughts without promoting and normalising rape cuture. But I don't even get the sense from Atwood that she even knows what's going on in the UK and has a reasoned opinion about it, just that she doesn't want to be hounded again. Can't blame her on an individual level, I guess - it just renews my respect for the few brave people (many of them here) who DO tell the truth. Imagine if we all did?