The ending is perfect.
Do you honestly think Joel would have sacrificed his surrogate daughter for some great cause like saving the world? Protecting one's family is a natural instinct that comes before general altruism. The fact that Ellie isn't Joel's biological daughter only makes the ending more poignant.
There are a lot of other little brilliant things about the ending as well: one of my favorites it how, when Marlene is sacrificing Ellie's life, she's doing it to save the world. But when she's begging Joel for her own life, it's not to save the world -- it's to save herself. She's just as selfish as Joel is. Everyone in The Last of Us is selfish, even if they're trying to do some grand altruistic thing.
Also, the last playable section when you're running from the hospital and the musical theme that played when Joel lost Sarah kicks in is literally one of the most moving moments I've ever experienced.
If I were in Joel's shoes, I would have done what he did without a second thought.
