I'd save Ellie. The world is only as important as the people closest to me and if 99% of people I don't know had to be sacrificed to save someone close to me, so be it, this will obviously never happen in my life so I don't fully know how I would react or end up making the decision but I know Ellie would not be a sacrificial lamb for the potential of a world that is already fucked, that's for sure. The fact that the cure is only a potential is also a strong reason I'd save Ellie. I wouldn't trust anyone who would say otherwise to be quite honest but at the end of the day, someone who could sacrifice Ellie without hesitation is the person who should have been chosen for the job in the first place, the black chick should have done it herself and if I were in Joels shoes I'd save ellie but it'd probably nag at me enough to drive me into a shell of a person afterward.
Everything in the above reply is my opinion, from my own perspective and not representative of reality outside of my own head!
-Android user, please be gentle with critique on my spelling.