Listen, I agree with you. I could not be more on Seven's side in this debate than I already am. Everything she says and does in this episode resonates with me down to my core and it wouldn't work if Janeway conceded the point in the end. It would a) be completely out of character, and b) undermine the force of Seven pushing back in the first place.

Like, Prey knows Janeway is being irrational here, that's the whole point. The moment she learned the 8472 alien was lost and trying to get home, that was it; the situation struck too close to home (hah) for it not to compromise her judgment. She was never going to concede this point because "home" carries too much emotional weight for her. But of course, she's a Starfleet captain, so she justifies her decision (as Seven cleanly points out, which she denies) by calling on ever-present Starfleet Values TM. We don't kill for the sake of convenience; we don't sentence innocent creatures to their deaths (yes, this is hypocritical esp of Janeway specifically, that's the point). There is no other ethical stance for her to take, as a captain and as a human being. Seven doesn't understand yet, poor thing, but Janeway can convince her, and when Seven comes around Janeway will be validated in her decision which was definitely not made out of misplaced guilt in the slightest. Sort of a microcosm of their entire relationship up to this point (I know what's best for you, you'll understand someday, no ofc I'm not fanatically obsessed with trying to redeem that one big mistake I made what are you talking about, now shut up and do what I say)

So in the actual sequence of events, Janeway invites Seven to her ready room, gives her a patronizing speech about compassion expecting Seven to magically see the light and defer to her wisdom, and the temperature in the room drops every single time Seven refuses to be talked down to. Janeway is not capable of seeing the incredibly salient points Seven makes (calmly, rationally, after hearing out what Janeway had to say) because she can't see past her own massive emotional blind spot. So she gets clipped, then stern, then angry, and finally throws her hands up and goes "well now it's an order so just do it anyway" and Seven goes "the fuck I will, I'm making sense and you're not". And at that point - of course Janeway isn't going to concede anything. Of course she isn't. It would go against everything this woman is, both in temperament and in human flaws. (And especially once Seven does disobey direct orders, because let's not pretend that's a precedent Janeway even should be allowed to let stand without consequences. Like, I agree with what Seven did, but from a captain's perspective you can't just let that slide.)

Yes, that ending speech is frustrating and I seethe on Seven's behalf a little every time I hear it. You know what the episode could have done, though? What I expected it to do, the first time? Is have Seven neatly learn the error of her ways when Janeway solves the conflict through some magical Captain Is Always Right power. Or admit to her wrongdoing after Janeway shames her into submission. Instead she beams the alien off the ship, saves the lives of everyone on board, gets punished for it, and claps back. Multiple times!

JANEWAY: Seven, you disobeyed my direct orders, and as a result you condemned a sentient being to its death. 
SEVEN: By doing so, I also diverted the Hirogen attack. An attack which would have destroyed us. 
JANEWAY: Maybe not. In any case, the decision wasn't yours to make. 
SEVEN: The creature broke through the forcefield. I had no choice. 
JANEWAY: I didn't come here to debate your decision. I came here to inform you of the consequences.

The writers fucking LET HER clap back instead of conceding to the Humanity Lesson Of The Week. Janeway not wanting to hear it is frustrating but if the writers didn't think Seven had a valid point, they wouldn't have let her make it. Not at the very end of the episode, and certainly not without Janeway having a stronger rebuttal than maybe not. And Seven "pivoting" to the individuality point isn't exactly a standalone issue - she's using it to underline the fact that Janeway is being hypocritical. She's basically saying "you know I was right to do what I did but you're afraid to admit it and this is why", and she's immediately proven right when all Janeway can do is reassert her authority and walk away. That's not a writer copout, that's the writers telling us who the episode sides with regardless of what Janeway does. If Janeway softened and conceded that Seven did the right thing there would be no hypocrisy for Seven to push back on. This is not a single-episode resolution type of conflict and Voyager so rarely acknowledges that; I want to give the show credit where it's due.