I actually quite liked the hospital level. Having quite a bit of experience in stealth games, I played throughout the game trying to avoid unnecessary killing (as Garreth from the Thief series would put it, 'killing is the mark of an amature'). It made sense to me, as Joel clearly disproves of Tess' bloodlust in the first chapter. It made it easier for me to connect to Joel's humanity in all of this.
But anyway, throughout the game, the worst atrocities seen were never caused by the infected. They're rather docile and rather easily controlled as long as you take the right precautions. No, it was always other humans doing really sick things. Way before the ending, it had already become a matter to me of whether or not humanity was still worth this supposed cure. Joel even openly asks if they should go through with it, just before they hit Salt Lake City. When it becomes clear that the Fireflies just want to off her to get to the cure, I made up my mind. The Fireflies were no different. Humanity itself and the Fireflies in particular weren't worth that kind of sacrifice anymore. Not by a long shot if you consider other colonies like Tommy's have no problems thriving regardless of the infected.
~
But then, there's also the matter of Joel's lie in the car and later again just before the game ends. At first I didn't get why he lied in the car, but I understood it a little better during the second time he lied. Yes, he kind of sees her as his daughter, and no that's not the only thing playing here. It's because of the time they had spend together that he had begun to understand her quite a bit. She leaps into danger and very nearly gets herself killed numerous times. Because she is brave? I don't think so. She explains herself right before the end.
After she and her friend first got infected and she had to watch her friend die.. she was just waiting for her turn to die as well. Classic survivor's guilt, she had already accepted, even embraced death, deep inside. Joel had already started to realize this on some level, probably long before they even made it to Salt Lake City. He tried to spur her on when he she got depressed and gave her reasons to continue, those promised guitar and swimming lessons. So by the time she wakes up in the car an they're driving back to Tommy's colony, his choice not to tell her the truth about the nature of the cure.. well I think you understand. She would probably would have happily accepted death as an option. There would be no way to know for sure what she or others would ever do with that kind of information. He simply had to lie.
But then, it's kind of like she knows what really happened anyway. When she asks him to swear that he's telling the truth, it doesn't sound like she's asking him a question. It sounds more like she's 'ordering' him to believe that IT IS the truth, reinforcing his own and by extension each others beliefs.
