What I asked myself was what would Ellie have said if she was given the chance to choose for herself. And I don't think I could answer that. On the one hand, I think she really wanted to help with the cure, on the other hand she has a very strong sense of self preservation, and it is extremely hard for someone to make a decision to die for the greater good. So I don't think either Marlene or Joel were in a position to say what Ellie would want and then act accordingly.
Ethically Joel made the right decision to take Ellie away, because Ellie was being denied that most basic of rights when it comes to invasion of a person's body, which is consent. However, he made a terrible ethical mistake in choosing to lie to her, simply because he was afraid she would demand that he take her back to the fireflies and let her die for a cure, or that having lost that opportunity to return that she would reject and resent him for making such a decision for her. That's where Joel's selfishness came in IMO.
“The fundamental cause of the trouble is that in the modern world the stupid are cocksure while the intelligent are full of doubt.” - Bertrand Russell
"When the power of love overcomes the love of power, the world will know peace."
Jimi Hendrix