Joel never trusted the Fireflies in the first place, and he was greeted by heavily armed soldiers before he even realized what would happen to Ellie - I feel like anyone here would be pissed if that happens. I also don’t remember any notable events where they revealed the scale of the Fireflies’ capabilities and operation, so we don’t even know f they were able to distribute the vaccines if they could develop one; all I remember is seeing Fireflies get killed throughout the game and never seeing them live long enough to do anything useful until the end