From what was said by Ellie at the end of the game she would have chose to die and she makes that clear. In the face of that he could have told her what really went down and accepted her reaction and decision on the issue. Instead he chose to double down on the lie for his own selfish purposes opposing her feelings on the issue. Joel is a piece of shyt and whatever relationship he has with Ellie going forward is based on a lie. That's not love it's selfish use of a person to fill a void in your life. At that point his need for her to feel that void was more important than anything else even being straight with her.
Joel probably couldn't take another loss of someone he came to undoubtedly love as his own after his biological daughter's death. I sensed he wouldn't let them take Ellie away at the end of the fall chapter where you ride back to the University via horseback with Ellie. Eitherway, there is DLC coming out for SP so it may be related to this or not The ending left me feeling ambiguous.