You mean you'd fuck Ellie? Yeah she's kind of cute and as long as you don't force her... But this is not what is asked here, also she's gay...
Anyway it's weird to see this question asked so many years after that game's been released but sure why not.
So I'd save Ellie any day, she is NOT responsible for what happens to mankind, it's NOT her job or destiny to die to save others. Killing her would be murdering a healthy human.
If you guys think life is just a mathematical equation where you can kill one to save others, you have serious issues with your moral compass, which is kind of expected from the masses I guess.
But... What about all of the other people you killed? A few, probably weren't even threatening you (yet). Didn't hesitate then, did you? So you can take that "holier than thou" attitude elsewhere, Joel!