I don't think you understand the characters or much of the plot, honestly.
Yes, Ellie in her youthful naivete may have accepted her sacrifice for the greater good, but there's zero chance Joel would've respected that decision. As evidenced through their discussion earlier, Ellie had given Joel purpose again. He was reconnecting with what it meant to be a father, and Ellie was becoming like a daughter to him. He saw her for the child she is, and knowing that, understood she isn't old enough to make a life or death decision on the spot. He would want to protect her, keep her alive, at all costs. Joel would not "have to accept her decision and go along with it", and he wouldn't.
Just because the Fireflies might have had advance knowledge that an armed man may at some point show up escorting a child doesn't mean they wouldn't mistake an armed pair showing up on their doorstep as possibly being a couple of raiders. They didn't shoot them dead in the street. They subdued and apprehended them, discovered who they were, and moved forward accordingly. Also, as to "where is everyone" when they show up - it's a secret lab. They wouldn't be bustling with activity because they're trying to avoid detection. You can see during the firefight that there is clearly staff there, but they're largely trying to remain incognito.
Marlene told Joel about the surgery because he went through hell and back to get Ellie to the Salt Lake. But the Joel that Marlene knew in Boston, who referred to Ellie as "cargo", was not the Joel who turned up in SLC. Marlene wasn't fully aware of the bond that had developed between them. She figured Joel was just finishing up another job, and would be on his way now that the job is done. Which would also explain why she didn't send more guards to escort him out.
You're severely underestimating how complicated brain surgery is ("just do a minor brain surgery"?), and at the same time overestimating the capabilities of the hospital. Understand that brain surgery is a delicate process under the most ideal conditions. The conditions in the Fireflies hospital are far from ideal.
This is a post-apocalyptic setting. Medicine, clean water, general supplies, resources... All scarce and hard to come by. They were discussing whether they'd even have enough power to complete the procedure. Add to this we don't know how capable the staff is. Dr Anderson seems to be fairly competent and confident, but even if he's the best doctor in the apocalypse, he may have been average during the time preceding the outbreak. They more than likely are working without all of the tools and equipment they normally would have or even need, and are clearly understaffed for such a procedure.
There was never any possibility of a "minor" brain surgery. The possibility of Ellie's survival wasn't even discussed because under these circumstances there was no possibility of survival. Ellie was going to die. And there was no chance in hell Joel was gonna stand by and let that happen. None.
As to the sequel, I'm not sure what you were looking for in an ending but Part II was brilliant. It showed just how costly vengeance and unchecked wrath can be, and how a vengeance sated does not necessarily assuage the pain and damage one is seeking to rectify. Ellie choosing forgiveness and mercy over hollow vengeance is possibly the closest thing we could get to a happy ending, given the circumstances. She's attempting to break the cycle, and in doing so not only puts herself on a path of redemption, but also moves toward redeeming Joel as a father figure. He's helped to raise Ellie to be a better person than himself.
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What's better than roses on your piano? A pickpocket that snatches y- wait, no... that's not it I messed it up let me try again...