Oop get ready for an unpopular opinion. I actually love that whole conversation and everything it illuminates about both Alicent and Rhaenys. It's such an effective and devastating commentary on the different reactions women have to the patriarchy. And I don't think it has to be read as Rhaenys antagonizing or looking down upon Alicent, in which case she definitely does come across as a hypocrite, given that she never once even attempts to disobey her husband no matter how strongly she disagrees with him.
But is that the only way to read Rhaenys's words here? No. And I'm not convinced she's trying to accuse Alicent of wrongdoing here, especially in light of the conversation Rhaenys had with Rhaenyra in episode 2. In that conversation, Rhaenyra very much seems to be reveling in the fact that she is an exception while Rhaenys is not. Rhaenys fails to rise to the bait, because she understands what Rhaenyra does not: There is no exception to misogyny, not even if you are the rightful heir to the throne. So it seems odd for Rhaenys to see right through Rhaenyra there, and yet to turn around and do the exact same thing to Alicent.
So I think that in episode 9 Rhaenys is commiserating with Alicent. Consider the actual words she says. Never once does she insult Alicent, or imply that she is evil for the things she's had to do. She simply says, "you toil still in service to men. Your father, your husband, your son." This doesn't have to be a judgment, since Rhaenys has spent her entire life doing the exact same thing. Remember, in this scene Rhaenys is trying to convince Alicent to free her. It's not unthinkable that she's trying to build common ground and incite Alicent's sympathy in order to get herself released. It's not unthinkable that she says this knowing the exact same thing applies to her, too, that she says this precisely because of it.
And consider the line "have you never imagined yourself on the Iron Throne" and how incredibly telling it is. Rhaenys isn't necessarily marveling at the fact that Alicent works within the limits of the patriarchy, because for all the above reasons Rhaenys herself very much does the same thing; she's marveling at the fact that Alicent is so brainwashed she doesn't even allow herself to privately dream of freedom. That she "desire[s] not to be free, but to make a window within the wall of [her] prison."
Because Rhaenys cannot stop imagining it, imagining herself on the Iron Throne. The indignity and cruelty and injustice of being denied her birthright haunts her every waking moment. Now, this anger does not give her the power to challenge what has been done to her. She conforms, and she submits, just like Alicent. But it makes her fucking furious, while Alicent will not even allow herself that. Rhaenys cannot be content with just a window, and she knows that deep down Alicent cannot be, either, but that doesn't mean Rhaenys thinks she's any less trapped within that prison. Rhaenys wants more than a window, and yet she knows that both her and Alicent will never be able to have anything more.
Rhaenys isn't marveling in how brainwashed Alicent is. She's sympathizing with it. Yes, she's frustrated and angry, but she displays enough awareness throughout the series to indicate that she'd understand Alicent isn't the target of her ire. She's venting, y'all, to the only other person who might understand her unique torment as a high-born woman whose power is still not enough to save her.
I know fandom loves to pit women against each other, especially in this case given the whole team divide within the HotD fandom. But in my mind, this is simply an excruciatingly honest and vulnerable conversation between two women who have spent their entire lives being trampled by the patriarchy, allowing it to happen because they have no other choice. They are the same in every way, and they are the same in their helplessness in the face of institutional misogyny. Alicent and Rhaenys are the same, save for how they privately feel about their circumstances: Whether they feel resignation, or rage.
And these negative feelings are levied not towards each other, because they both understand (unlike baby Rhaenyra in episode 2) that other women are not and have never been the enemy. Instead, these feelings are directed towards the men, towards the patriarchy, towards the system that has actually done this to them. Rhaenys is furious in this scene, but I think it's so much more interesting if you recognize that she is only ever furious at what the patriarchy has done to her, and that the only things she feels towards Alicent are camaraderie and pity.
HotD is a fascinating exploration of all of the different ways in which women try to respond or cope with the patriarchy. Alicent, a noble but relatively unpowerful girl, spends her entire life submitting to the more powerful men around her, telling herself she's alright with how things are. Rhaenys, one of the most powerful women alive, the rightful heir to the Throne and a dragonrider to boot, spends her entire life submitting to her more powerful, male family members, raging internally the whole way. Rhaenyra, arguably the most powerful woman alive, the rightful heir to the Throne and a dragonrider with the backing of all of the men in her family, fights and refuses to accept that things have to be this way. And yet all of them still suffer.
GRRM shows that no matter how much a woman conforms, and no matter how much a woman rebels, and no matter how much power a woman has within the system, the system will always win. No single person will ever best a centuries-instilled institution of oppression. This is also the reason why Daenerys succeeds, where these equally intelligent and talented women fail: Because she dismantles the system of power entirely. Because she breaks the wheel.
