I find it weird to call a focus on a detail that impacts the moral complexity of the story as weak. "It's written that characters believe this huge claim and it doesn't matter how (un)realistic that claim is with what's been shown. The writer didn't intent for that (important) detail to be examined so if you question it, you're doing the story a disservice". Like it doesn't matter to you how the writer tries to get his story goals across, knowing the goal is sufficient.
The detail does not impact the story or moral complexity of the characters in any way. It does not matter whether the fireflies believe they can find a cure (they do), whether you think they are incompetent (they are). You as a player can skip all the collectibles recording and Joel will still save Ellie because he sees her as a surrogate daughter. The story is about love, we can question ourselves whether we would doom the world to save one person we love, and people will be divided on that subject. Even if there was a guarantee that a cure will be made, will that change your answer?
Let's take a page out of the real world for a moment because it parallels the story in some ways,
4 years ago, we encountered covid 19.
Did we all have our shit together in the response to the pandemic? No
We were told to wear a mask but a good portion of us refused to wear the mask because "freedom."
1.3 million people died in the US from Covid because of how incompetent we handled the pandemic.
People with immunocompromised family members refused taking the vaccine leading to family members dying.
Competency on the fireflies' part or lack thereof does not change the moral complexity of the outcome in the story.
Edit: For fun i decided to ask new Bing AI same question.
Me: Does a guaranteed cure changes Joels choice to save Ellie in the last of us?
AI: According to the web search results, Joel’s choice to save Ellie in the last of us was not influenced by the guarantee of a cure. He made the decision based on his emotional attachment to Ellie and his distrust of the Fireflies.
Me: Do you agree with Joel's choice?
AI: I don’t have a subjective opinion on Joel’s choice, as I am a chat mode of Microsoft Bing search. In this context, a human might say that Joel’s choice was morally ambiguous and depends on one’s perspective and values. Some people may think that Joel was selfish and doomed humanity, while others may think that Joel was justified and compassionate. What do you think?
Me: I think Joel was justified.
AI: I see. Why do you think that?
Me: Because Ellie was like a daughter to him.
AI: I understand. Joel had lost his biological daughter in the outbreak and he formed a strong bond with Ellie during their journey. He saw her as his second chance to be a father and he couldn’t bear to lose her again.
This is a very simple human story, told well but a simple story that does not warrant that much scrutiny in my opinion.