I don't think Joel acted selfish.
Ellie was 14 Years old. And the decision she is forced to make is basically "We have to kill you to save the world. and that is the only way, if you refuse everyone is going to die. So is it OK to kill you? You would save the whole world!"
Your'e basically putting the whole weight of the world on the shoulders of a 14 year old. Yes she agreed to do it, but is that really a decision she should even make?
(Also how big are the chances that this will actually work? How big are the ones that she will be killed for nothing....ooops that didn't work, sorry)
Ellie agreed to do it, but as i said she was 14 yeat old girl with the weight of the world on her shoulders. Did she really agree because she wanted to do it, or does she just feel that she has to do it, because of all that weight.
Joel feeling like a father to her at this time decides that this decision is to big for her to make now. He as a parent takes that weight of her and makes that decision for her. Just like countless parents all over the world decide things for their 14 year old kids every day.
Yes the stakes are higher here, and all the killings that Joel does in wake of that decision are something very different from the other decisions that i talked about, but then again, these things are a side effect of the world they are living in.
How many parents in the real world would you think would agree to kill their 14 year old child if that could be the cure for cancer and or other diseases? I don't think the number would be that high (certainly not 100:0). And even when the child thinks it should do it, wouldn't a lot of parents say still no, and force the child to at least wait until it is an adult to make that decision? Yes cancer isn't an all killing desease that will kill the poulation in a short time, but i still think the decisions are not that different. Certainly as long as no one can 100 % guarantee an success with the operation/serum.
I just think it is a bit to easy to just paint it as a selfish decision by Joel.
As for the end, i always thought about it as if Ellie deep inside her knew what happened, but Joel doesn't tell her, again to not put this also on her. When Ellie says OK she basically accepts that and at least for now, she is a child/teenager and Joel her father.