Again, Ellie makes it clear she was ready to die even before she got to the Hospial, the "If we get through this we will do X afterwards" is a very common trope in fiction, a very common death flag as well, specially when coupled with the "longingly look to the horizon, before solemnly declare that they are not backing down", and everything about the framing of scenes and her tone of voice are very by the book "This character knows they will die afterwards" if I have ever seen it happen. And again, she afterwards makes it clear she expected to die, what with stating she now is "Still waiting for her turn".
Were the Fireflies good guys? Not really, they have the same violent demeanor as all the post poacalyptic groups, and obviously engaged in immoral actions, and they were ready to kill Joel. So they aren't exactly "good guys".
The thing here is that Joel not only took her choice from her (The director even stated this is the intention) but also on top of that action also lied to her for years and engaged in classic abuse tactics to cover himself. And in the end his actions doomed humanity to never being able to get rid of the fungus contrary to the wishes of the girl he "wanted to protect", her last question to him at the end of the game is very clearly her giving him another chance of telling her the truth, because she knows he was very clearly lying, and he again repeats the lie, with the last shot of her face disappointed, when she tries to talk to him about her feeling post the "failure of the vaccine" he doesn't even attempt to hear her out fully, he cuts her off to tell him what HE THINKS she should think.
The game even uses the language of gameplay to communicate that Joel is no longer the POV, that he is not the hero anymore, there is a small gameplay sequence that seems out of place, you control Ellie in a brief walk, he is always far away, he only talks to compare Ellie to his daugther and guiding you, due to the lighting his face is mostly framed in shadow until the last moment when Ellie talks to him. After this you never control Joel Again, even in the DLC.
Also in the end both the Doctors and Marlene attempt to plead to him, to relent in his rampage and think it through and he doesn't. He doesn't even seem to care if the Fireflies go and scoop someone else's brain out for it "Find someone else" is his answer, basically do it with someone I don't care about.
And yeah, he is kind of a dad psychopath, as after finding this out Ellie can't even stand being around him as shown in the Last of Us 2.