I would save her and there are a few reasons why.
1.The fireflies, to me, are not as pure and caring as they want to be. They spoke noble and whatever, but at the beginning of the game, they launched an attack on the military (when Joel and Tess were trying to exit the QZ) They also wanted to kill Joel after he took Ellie all the way to them (granted, marlene said otherwise)
2. Is the world truly worth saving at this point? It has been 20 years since this happened. So far, people have been killing, murdering, eating each other, raping and etc. Even with a cure, you think they can ever go back to bein civilized? The exception to this is Tommy's camp, who actually got electricity, a gated community, etc but that is a tiny minority. The rest of the people, in my opinion, are too far gone.
3. I don't think they fireflies had the means to distribute the cure. Also, they are in direct conflict with the military. Do you really believe they would simple hand them the cure wrapped with a bow and everything? Of course, they would use it as leverage to get what they want.
I'm probably over analyzing, but either way, I felt a bond with Ellie that I could not have let go just like that. Joel is no hero and the ending shows it perfectly.
"Trick shot? The trick is NOT to get shot." - Lucian
