Beware, massive spoilers ensues!
I won't speak for anyone other than myself when I say that I absolutely loved Ellie. She was feisty and could hold her own, or how David said it so wonderfully; she has heart. However, would this adoration I have for this girl compel me to deceive her?
Throughout the game she became someone she didn't want to be, but (apocalyptic) circumstances demanded of her to be that person she dreaded, a coldblooded killer. Her greatest wish was not to take lives but to save them. She accepted to be used as a tool if it meant humanity's survival. And yes, Joel loved her dearly. He saw the likeness of his daughter in her and perhaps came to see her as some kind of substitute for his loss, but is that an excuse for his selfishness? Once again, Ellie had a clear goal and that was sacrificing herself. I think it would be safe to say that it was her dream, her own reason to fight this long so she could save lives. And Joel took that away from her. They both didn't know that Ellie's death would result from creating the vaccine. Joel found out while Ellie was out the whole time, but would it have made a difference if Ellie knew? I think she would've carried on with it, even if it meant her death. If stealing humanity's last hope isn't bad enough, he lies to her in her face. You could see she was agonizing over it, especially after she told her story about her best friend. She was waiting for her time to come. Little does she know.
I can understand Joel's motive, but I don't agree with it. It's plain selfishness. Ellie's death would've been a sad thing but also a good thing. The world would've been saved and she would've been happy about that. Instead, now she will live her entire live in discontent thinking 'what if?'.