Yeah Marlene's choice to rob Ellie of her own choice is what lead to this.
My take is part of the moral dilemma is the implied double standard.
Let me explain by running a hypothetical.
Situation A - You have no kids. You have no romances, no ties, no debts, no dependents nor obligations. It's just you in a screwed post apocalyptic world full of clickers, FEDRA and Fireflies. The issue of Ellie having a choice has some impact on your life, but you can decide for yourself what measure of risk you will accept for yourself.
Situation B - You had three kids. Two already died from infections/clickers/attacks. Your youngest is still alive. Having Ellie be operated on and sacrificed works as a slim chance that a "cure" can be found, thus giving all of humanity some measure of hope. But by extension, also giving your last surviving child a better chance to survive and maybe even, one day, to thrive.
I have a young nephew. If he was in Ellie's shoes, i.e. as "The Cure" Then No, I wouldn't accept him getting lobotomized even if the entire world had to burn over it.
However, if it was the child of someone out there or even here was that same cure, and their sacrifice would give my nephew a fighting chance at a decent safe and productive life moving forward, then I'd literally pick up that kid, and toss them into a woodchipper if I had to do it.
I readily admit I have a double standard here. I'm not trying to be fair, if some will say that's not fair or hypocritical. If they or you called me a hypocrite, I'd agree. I'd admit it openly. People can call me whatever names they want, as long as my nephew is safe. Some people here are parents, or they have younger siblings or cousins or nieces or nephews, that kind of thing. They see where I'm coming from with all this. What I'm saying is not from a place of malice. It's not like I'm advocating going around hurting kids for sport or for no apparent reason. But blood is blood, nothing else is it's equal.
If Ellie was the cure, and Sarah was still alive, does anyone think Joel wouldn't literally crack open Ellie's head on his own, if he had to do it, to try for that 1/10000th percent chance of finding a cure to keep his real biological daughter safe?
I do believe though, for Joel, there is a lot of complexity here. When he was arguing with Tommy, Joel points out that they did what they needed to do to survive ( i.e. a rationalization) whereas Tommy simply said, "There were other ways" But Tommy has that luxury, because Joel was the one who was responsible to lead and make decisions. It's easy to choose the virtuous path when it costs someone less. What happens if it costs you more?
So I'm not trying to pick on you here. I am however saying the show and this story creates a pretty fascinating moral quandary.
My view of "right versus wrong", and no one needs to share it, comes down to what I can sleep with at night. And I can sleep with a lot. And for my nephew, I can sleep with even more. You could fill an ocean with what I could sleep with if that's what it took to keep him safe from harm. And I suppose that's part of the tragedy. That one could inflict so much hate and bloodshed upon the world for the sake of unconditional love.