The purported cure stops people from getting infected (it doesnt cure the already infected as far as I can tell).
Terminology check: That makes it a vaccine, not a cure. And it's an important difference.
Bites from infected turn from 'always lethal' to 'painful and annoying'. The infected can be safely hunted down and killed with far less risk than at present, and an encounter with one is much more likely to wind up with the human still alive.
No more people get turned into Zombies.
Eventually, assuming nothing else happens in the meantime, like a particularly bad strain of flu or a terrible winter that kills off the crops, etc.
But if all of that happens -- and it's a big, big "if," given that medieval Europe had several times it was pushed to the brink, with many more resources than the post-apocalyptic US on the show has -- yes, in years or decades, the fungus would be wiped out.
Unless, of course, it mutates again.
That's not the choice Joel has to make.
The choice is 'murder a bunch of people in a mass shooting spree, lie to Ellie, deprive her of agency and the choice she likely would have made herself, and potentially doom humanity - and millions of people - to the zombie apocalypse' vs 'leave her to die at the hands of the Fireflies, who might potentially be able to save humanity and millions of innocent people via her death'.
That's Joels choice.
I'm not saying I agree with Joel's choice, but
no one is giving Ellie a choice, so he doesn't come out worse here than the Fireflies do. We don't really know what choice she would make (yet) because no one has been willing to ask her.
So, his decision is "do I kill these people who are mostly strangers, and a frenemy of mine, or do I save the life of this girl I love."
He is a profoundly broken person who has chosen violence for more than a decade at this point as one of his ways of medicating. He has decided, incorrectly as we see, that he's fixed now because of Ellie, and the moment that's threatened, he goes completely off the rails again.
TV watchers, and maybe game players, don't know enough about these other characters to know about their level of dysfunction, but we know that Joel is a mess. I think Marlene realized in the waiting room that entrusting Ellie to Joel would inevitably lead to a situation like this, since she appears to know at least somewhat about his past.
The story is a tragedy all around. And like the best tragedies, everyone is doing what they think is the right or only choice in the moment, even when an outside observer can see otherwise.
