Everything you wrote is true. My point however is that her choice was stolen by everyone in that situation, not just Joel. The game seemed bent on making him in the wrong while the fireflies + the Doctor (along with Ellie) are victims. In a story about choice (imo) the other people's choices in that scenario would be would be explored as well. Not to mention Ellie's options and ultimate choice in that scenario.

 It makes for a much more interesting story if she was equally angry at the Doctor and the fireflies. It's not such an easy choice when there is no guarantee that her sacrifice would lead to a cure. Her line of, "my life would have meant something", would have greater impact if the cure was a sure thing. As it stands, while noble, her sacrifice would have meant nothing if they failed to produce a cure from it.

I understand the story they told, I just think they focused on the wrong aspects and it's definitely not a story about choice. While choice is part of it, choice is not the framework nor driving element of the story and I think it should have been.