I seemed to have interpreted something very different about Joel's character and the ending than most. To me, Joel was a broken man projecting his feelings for his daughter onto Ellie by the end, and he didn't see her so much as her own person but something to protect. He wouldn't talk to her about the traumatic deaths she witnessed and called her 'Baby Girl', just like he did his daughter, as well. It was most evident to me in the ending, though. He never considered what she would have wanted, making the decision himself, and even lied to her when she asked what really happened. I never got the feeling that he genuinely cared about ELLIE so much as cared about doing whatever it took to prevent losing his daughter all over again.
Edit: I guess I should answer the question in the thread title, huh? I would have drawn my weapon and demanded they allow Ellie to wake up, and tell her every detail of what was going to happen, and what the outcomes would be. It's unfair to make the decision for her, but it's also unfair let her make the choice uninformed.