For that to work I feel there should've been some explanation why the surgery needed to happen the way it did but there isn't which makes the Fireflies look bad.
The explanation is the mutated cordyceps is wrapped around her brain meaning there's no way to extract this benign, mutated version without killing Ellie. This being the first and only medical examination is why the decision to continue or not has to be made quickly. The Fireflies have been decimated at this point making it a last ditch attempt at creating a cure and thus rebuilding their bargaining power.
It doesn't make them look good, but then nothing the Fireflies do really makes them look good. The only question is whether they represent a greater or lesser evil than the authorities, who themselves are in equally dire straits at this point.
It would make it easier to paint Joel as (more) in the wrong if there was.
To Abby, the problem with Joel is that he murdered her father, not that he denied the world a cure. Its a personal vendetta.
To Ellie, the problem with Joel is that he betrayed her trust and made her live a lie for years. Its a personal grudge, and him being killed by Abby before they have properly reconciled their issue is what hits her the hardest. That Joel would have enemies from his past who'd like to do him harm is no surprise at all, its the timing of it that really hurts precisely because Joel's reasons for saving her were understandable, even if they were selfish.
Joel is still Joel. There's no revision to his character or outlook at all, he states repeatedly that he'd do it again. Even if he knew the cure would have been a success he would still have chosen the same path. In some respects he's like Rorschach in Watchmen, his past has rigidly bound him to follow his convictions beyond all reason or debate. Its a sort of broken heroism that is simultaneously admirable and tragic.
Stop looking for a moral lesson here. Its just human behavior in extremis; desperate people clinging onto their dreams and values in world that's long gone past the point of caring about any of that.
Assuming she was fine with dying regardless of what she went through with Joel, don't you feel that's a bad outlook for Ellie's character? That she's OK with leaving Joel so abruptly? That doesn't sound like the Ellie we see throughout the game.
But we know she's damaged emotionally. Orphaned, forced to watch her first love die before her eyes while she inexplicably survived. She's untrusting and defensive, but over the course of their long journey together to Salt Lake she opens up and bonds with Joel as the reliable parental figure she's always craved. She's forced to kill or be killed, brutally stabbing David to death before he rapes and murders her.
By the end of the story she's distant and obsessed with the journey, and her life to that point, actually meaning something. There's a brief moment of respite with the Giraffes but that's just one moment within an endless fight for survival.
So no. It exactly sounds like the Ellie we see at the end of the game. Confused, doubting, underwhelmed by the prospect of life in Jackson, and still tormented by an existential need for her immunity to mean something.