I think Ellie was remembering all the people that sacrificed their lives to get her to the Fireflies.
Actually, it was all the people she knew who got infected and died since she was bitten, hence her strong motivation to help create a vaccine.
Not only did he lie, but he killed the surgeon who may possibly be the only person that can fashion a cure.
You don't actually have to kill him apparently. It's funny how many people just shot him, or even the whole medical staff, and assumed that's just what you were supposed to do.
As for the rest of the ending, I can't help but think its worth saving the life of the one person who's willing to lay down her life for the rest of humanity over the people willing to kill a young girl to save themselves.
I really wish I could play this game myself, rather than having to watch let's plays of it.