So, I would have a lot more sympathy for the 'Joel is a monster who damned the world' spin, if they didn't make it the absolute worst position possible for him. He is attacked, wakes up in a prison cell with none of his stuff. Ellie is missing. They tell him Ellie is going to get her head cracked open and die for the 'greater good.' He doesn't believe in the scientists really, cause why would he, he has no proof? And they are jumping straight to 'lets crack her head open.' and not like, lets draw samples and test. Also, they have him in prison with none of his kit, and are basically unspokenly threatening him. He asks to speak to Ellie, to get her confirmation. They refuse. So now he doubts that its her choice as well and has reason to believe she is now being murdered against her will. They make no attempt at all to better the situation, and from his point of view I would totally see them as people who are going to murder a young girl for their revolutionary ideology and hope of finding a cure to use it to not only save mankind from the disease but also usher in a 'better age.' Joel doesn't believe in the Fireflies. He never did. Given his complete lack of faith in such groups cause of his history, I see him as having no other real option that is acceptable.
Add to that the journal entries from the woman who was Ellie's caretaker, where its rather obvious she herself questions her course of action but sells herself on the faith of the ideology and saving the world? The Greater Good? Yeah, they could have done a lot of things to smooth over the situation with Joel, but they didn't and I can't really buy they were looking at a high probability of success.
On its face, its a 'the good of the one vs the good of the many' combined with Joel's apparent selfishness, but I can't help but see the Fireflies as being selfish and fanatical, committed to their ends no matter the cost. You see that at the very beginning when Joel and Trish are talking about the Fireflies terrorist attacks on the food center, iirc, and there is nothing shown to change that opinion throughout the game. That was one of the things I found interesting about TLoU. The Fireflies are the 'good guys' but only because of their propaganda. Their actions don't really seem any different and there is nothing to make you think they are actually 'good' presented in the game. Just propaganda broadcasts and flyers.
Edited to add in, cause I just remembered. He was attacked /while giving rescue breathing to Ellie/. If I recall, he actually asks for help from them and they beat him. That is not the action of people who you would trust and have faith in. They are not the good guys.
