That's difficult to answer to me.
On one hand a person I love as my daughter. On the other one the possibility to help the entire humanity to survive.

So, because she wasn't his biological daughter it means that she was not his daughter to him at all? They spent a whole year together, surviving, taking care of each other, acting as parent and child (Joel teaching Ellie stuff and Ellie getting mad at Joel for acting all "you were just an errand"). I don't know about you, but they were pretty father and daughter to me.

Joel didn't kill a bunch of people that were trying to find a cure, he killed a bunch of people that wanted to kill his daughter, if you know what I mean.

I also don't think it is that easy to compare the value of life and sacrifice by the mere quantity of lives being traded. Each person is unique, and in their uniqueness they all have yet other layer of uniequeness by each person they know and that cares for them. The value of life is not comparable like that, unless you strip yourself from that thought, which is easy to do when you don't know and/or you don't have any real feelings towards any of the people you are rulling a judgement on, but when you know that person? When you love them? When you would die for them? To expect others to sacrifice all they have for you to keep what you have is in itself selfish, in my opinion.

Also I'm not saying that I wouldn't want for some other parent to sacrifice his child for me to keep mine alive, but I'm not going to say or act like I would be fine or cold enough to just be like "1000 children > my children, fair enough".

I don't think it is about being nice or not, maybe it is just difficult empathizing with the love a parent feels for their children without having felt it.