1) About the bond he created during their journey:
She has this bond as well, mind you. She witnessed all this shit by herself, too. And yet, she STILL wanted to help humanity. She is a teenager and yet smarter than an adult. She still sees the bigger picture while Joel is a selfish madman.
2) About the hurdles of distribution afterwards, and the slim chances of success altogether:
Yes, problems may arise afterwards, but humanity would still be one step closer to salvation no matter what. The premise would be much better anyway. Even when the chances are small, you still need to try it, especially in extreme situations like in the game. Saying that the problems are too much of a hassle so let's cancel the one year trip with the many, many sacrifices already done is terribly selfish and lazy. The moment you stop trying is the moment you instantly lose.
I mean, what kind of bullshit have they been through all this time? How many battles had they been through? And yet, just before the end of it all, just before they reached their goal which they have been working for throughout this entire trip it all suddenly becomes meaningless? Really? This is stupid! Joel had more than enough time to get accustomed to the idea, but NO, he just decides to shit on everything, do a 180 and ignores her will just so he can keep travelling around with her because he likes it that way. What kind of nonsense? He not only destroyed the slim chances of success, he also forces his will over Ellies.
Gameplay > Graphics
Substance > Style
Art Direction > Realism