Armin's reaction to having to kill that woman to save Jean.... I feel so bad for him. It was necessary to save Jean's life, and like Levi said, now that it's happened Armin needs to reconcile that with himself. And he said "thank you" to Armin. Don't think he's said those words before, or if he has I don't remember.
And Jean, he wasn't wrong for feeling the way he did. Far from it. He's in a difficult place because his morals and his duty are conflicting.
Of course, with Titans being humans he was going to have to face this conflict eventually. I'm still wondering why Levi hasn't brought this up with his squad (or maybe he has? but there's been no indication that he's passed the theory on). Perhaps he's decided that even though he suspects Hanji's right with her theory he doesn't want to concern his squad with it until it's proven true.
Good to see Marlo and especially Hitch back. Jean's test threw me off big time. Given what he was saying to Levi when the group was talking (when Jean was feeling guilty and Levi only said he was wrong for endangering his friends, and not wrong for feeling the way he did), I thought he had snapped and over-corrected for a minute there. He was lucky. If Marlo wasn't truly honest about his intentions to help them Jean would be dead. There was no one there to save him this time.
And with Hitch back and Annie being brought up again, I'm guessing she'll come back soon (yay!). Hitch seems like a nicer person than originally shown, and despite her attitude it seems like she does care about Annie and humanity. And she came back to save Marlo even though she was mean to him at first.
There is some definite friction between the regular MPs and the Interior MPs with Erwin's friend worrying about the Interior MPs possibly turning on them some day the way they are currently targeting the Survey Corps. Maybe the Survey Corps will gain some new allies?
As for the morals of what's been happening lately... With what Levi told Jean about Jean not being wrong and Jean's reaction to that, I don't think all of this is going to get written off as entirely justifiable. There's likely going to be something that comes up that shows that it wasn't entirely worth it even if they do succeed. That exchange is yet another indication that Levi, Hanji, and Erwin (and by extension, the rest of the Corps) are all aware of what they're doing and that their actions are bad even if they are fighting for what they believe to be the greater good (humanity's survival and freedom) as well as their own survival. Marlo also comments on what happened in Stohess as being "abhorrent", Hitch confronts Levi about it and he replies that he's aware of the consequences of what they did, and Erwin himself even admits that it was the lesser of two evils.
Related to some of that, Jean appeared worried that Levi would decide they needed to kill Marlo and Hitch, and looked relieved when he said they would let them go. Hanji and Levi also let Sanes live. Hanji was visibly upset over the torture incident. Erwin states during the Stohess raid that he's aware of how much Levi hates this stuff, and then there's Levi's retort of essentially "hating both dying needlessly and causing needless death". They're avoiding killing as much as they possibly can. Because they don't want to. Because they know it's wrong. It's just that there are times when deadly conflict is unavoidable with what they're trying to do, and they have to both accept and deal with that.
To be honest, with the way things are being portrayed I'd be surprised if Isayama tried to write everything off as 100% fine. He hasn't been glorifying these actions. Everything we've been shown has been absolutely horrific and gruesome and the characters being upfront and admitting that.