You should also try to account for what I was saying that in response to. Regardless, the revenge story in this world doesn't really fit given how many people have had to kill each other and the countless lives both Ellie & Abby took on their journeys and in Abby's case, her 5 year quest for revenge; if they wanted to make some sense of it, it would have been better if Ellie faced the infected (and it doesn't just have to be 'clickers') so it doesn't come off as odd when she decides or realizes that revenge is "folly" and let's Abby go. Yes, she's immune. But she isn't invulnerable.
You're grossly simplifying the reasons why the end of the game plays out like it does. Killing Mel is pretty much Ellie's breaking point; accidental or not killing a pregnant woman is unconscionable. Doubly so because of Ellie's personal situation (escorting Dina) and the presupposition that her quest for revenge has a moral justification as its basis.
Moving beyond that point and continuing to hunt Abby requires complete submission to rage over reason.
As things pan out, she doesn't get the chance to back out cleanly because Abby and Lev show up; at which point the similarities between them come into sharp focus. She knows why Abby came for Joel. She is somewhat "humanized" by her hurt at the loss of her friends, and the fact that she is swayed by Lev into sparing Dina and her unknown child as well as herself. Abby offers Ellie a glimpse of what awaits her down the road should she survive.
The reason for the about-face and deciding to pursue Abby and Lev to California is not a matter of choice for Ellie. She is suffering from PTSD and is functionally broken by the forgoing. She needs to confront her fear, her failure in order to move on. Abby is the focus but its not about her at all, its really about Ellie herself, her unresolved guilt over her estrangement for Joel, her inability to protect her friends and loved ones, and above all else her failure to confront her own fear.
Deep down, Abby is no longer the "other". She's not a mystery or some kind of quasi mythical "Moby Dick"; she is an externalized manifestation of Ellie's (and Joel's) inner darkness and turmoil.
This is why confronting and subduing her is enough to finish it, and why killing her is effectively an act of suicide.
I think killing of Joel was a risky/gutsy move. They just didn't pull it off well. I really think that the Walking Dead shock factor affected decision making for The Last of Us: Part 2.
I'm not disagreeing with you entirely, especially as I found the pacing issues to be most damaging in the first third of the game. It is kinda lumpy, but to a large extent that's a product of how the needs of the narrative bump hard against the needs of it being a game. Its the deep issue that anyone trying to craft a cinematic-style action game inevitably has to face up to; interactivity demands tutorialization and exposition for its systems and mechanics, which requires a different flow and cadence to that which communicates the narrative and characterization to its best effect.
Its quite a head-scratcher, and I know this from experience.
Similarly, considering this underlying issue, I find that organizing the story structure differently would lead to potentially worse problems for both gameplay and narrative. Its an old complaint of mine, lay people tend not to consider the consequences of their "obvious" fixes. They see a problem, mentally decide what they'd do differently, but don't think through how that change impacts everything thereafter.
In the long-run, that's been a major reason for why I've spent so much time arguing/defending the game, because as someone with familiarity with the process I can see a clear pattern of thought in their decision making process. Which isn't to say that I agree with every creative choice, just that I can imagine being in the room and hearing the arguments made for and against particular approaches.
