The vaccine is al but guaranteed if you collect al the audio files: There is one that states that there have been a dozen of trials to extract a vaccine from someone who was immune. They all failed and there is no guarantee that extracting tissue from Ellie would. What is sure is that it will kill her. So the options boll down to sacrafice a Child for a small chance of extracting a cure and an even smaller chance to succesfully spread it a cross the country. Just imagine the monopolyposition in a world as scattered as the last of US if someone had a cure. No way that would get distributed fairly. Or to save a Child against her own wishes and believes. I would change the latter.
This is basically why I would save her.
It’s not a simple question of saving Ellie vs. everyone else (in which case I would most likely concede that she is worth the sacrifice).
The successful creation of the vaccine was in question. Then the likelihood of unbiased distribution. Then the benefit of immunising everyone is doubtful, given the number/percentage of zombies created (who are deadly without infection). Then whether there was humanity left enough to save?
Given the circumstances, Ellie living on as a decent human being is a bigger contribution to the survival of our humanity.