I generally enjoyed the show, but Joel's decision had no meaning as it wasn't really a choice. It was easy to do what he did with the way they made the show. That shouldn't be the case.
Really? As a viewer, did you really need to be shown the threat several times to accept that it was a threat? I get it, it's usually better to explain stuff in visual ways rather than through exposition, but between being told repeatedly about the threat, the destruction of every city we see, and plenty of infected in the show (albeit front-loaded), I'm not sure it's fair to say that there was no real choice, or that humanity was fine either way.
Frankly, if anything undercut Joel's choice, it was the Firefly hospital itself. It was a bunch of armed thugs, one doctor and two (maybe three?) nurses. Joel was greeted by a grenade and being knocked out. Ellie was immediately taken to surgery, without a choice. Nothing much was really established about the doctor's credentials that I remember. Is this a high-end vaccine research scientist, where there could be some hope for success? And since medical ethics seem to be dead, wouldn't the Fireflys have simply injected pregnant mothers on the verge of giving birth with the fungus, most likely against their will?
Joel has no reason to trust this one doctor / scientist, especially after they demonstrated that they don't care about informed consent. Even if there were infected in every scene, Joel shouldn't let this particular dude cut up his surrogate daughter.