Testing her doesn't mean killing her. He thought there might be some non-lethal way. I imagine he never fully thought about it, he got shot at a lot

There was no way they were going to let them go. They let Ellie go, but they tracked her to get Joel. She was so fiercely loyal to Joel that she was not going to work with them while they were going to kill/eat him.

I don't think we are meant to think of Joel and Ellie as the "goodies." It is all grey

I realise his ignorance was essential to move the story along and provide that emotional conflict of interest that defines the end, but it seriosuly is something that he should have realized sooner. My take on it anyway.

nobody thought they were going to kill her, it was always thought to be just testing. even marlene didnt know until the end when they had her and made the initial tests the doctors found out the only way they can get a vaccine is to basically kill her, this is what happens when you only watch the cutescene's. in one of the recordings you find during gameplay you find one for marlene, she talks about how she got informed that they have to kill her and how she is struggling to make the call whether or not to do it, marlene promised ellie's mother to take care of ellie and she wouldnt have sent her if she knew she would have to be killed in the first place, even at the end of the recording you can hear her say why she accepted and gave the green light to the doctors, because she is tired, not because of humanity, not because its the "right" thing to do, its because she was tired of the situation, she cant handle it, it was marlene who was selfish, not anybody else. the firelies initially thought they just needed blood tests and what not, everybody thought it was just a matter of tests and nothing would really happen to ellie. 

Joel most certanly isnt a goodie. We find that out in the first hour of the game. Ellie is more complicated

Marlene also said that when she found out , them asking her to greenlight the procedure was just a formality and they would do it anyway regardless of her decision.

@ sales2099 , Regarding knowing they could kill her , lets not forget that joel and tess where only going to drop ellie off to the  fire flies and it was only tess's plea that got joel to continue on with ellie , so for much of the story you had a joel who had walled off his feelings treating ellie as a package to be delivered so there was no reason for him to delve into possible outcomes regarding ellie post delivery , plus most laymen would assume that they would use her blood or what ever to make a vaccine and that's exactly what I thought, also surviving the journey and even finding some fire flies alive where much more pressing concern's , rather than a subject that only  came to the fore at the hospital.

Reducing this game to good V evil is totally missing the point. It's about the difficult choices we have to make as people and as parents.

Honestly, I don't think Joel put much thought into the whole Firefly/vaccine thing because for a long time, he didn't want any part in it. He reluctantly takes on the job due to insistence from Tess, and only continues it for a time out of obligation to her, and even tries to dump the responsibility of transporting Ellie onto his brother. Even when he finally decides to help Ellie of his own volition, he still asks her if she wants to turn around, instead of completing the journey.

I think that it's clear that he really didn't care one way or another about the vaccine (and thus didn't seem to give it much though), not to mention that it is a bit of an assumption to expect Joel to deduce that Ellie had to die to study the immunity without more information.

To add some new thoughts I had over the last few days (I finished it on Monday and its still in my mind!)

Ok, at first I didnt like that at the end Joel lies to Ellie, and I will come back to that in a moment, its not that I didnt like the ending, just that these two people had become so close yet he still lied to her. But like someone else said, Joel isnt a nice guy, he is a survivor and does what it takes to survive. You see it as he mercilessly kills numerous people, tortures them, trusts no one, and its mentioned by Tommy when they meet up.

At the start of the game Ellie is very open and has that 'innocence' about her. By the end of the game, and having seen and survived through so much in their travels she has become the complete opposite, like she has lost faith in humanity, less trusting. For example, when they reach the hunters and that guy comes out feigning injury and calling for help, she wants to help him. By the time she meets David, even on first sight she doesnt trust him, and is willing to shoot him down at the first sign of trouble.

Joel on the other hand starts off as closed off, unwilling to let people get close, and trusts no one. Perhaps that was just something he felt towards Ellie due to how he lost his own daughter, and even failed to protect her. Also dont forget, when his daughter died, the world had just begun to fall apart. Yet they managed to excape the 'perceived' threat of the infected, they was at the home stretch and yet he lost his daughter to another human, the infection wasnt to blame.

From this moment on he did not trust anyone, and who can blame him? if I just escaped armageddon, reached what I thought was salvation only for the 'civilised' to turn on me, why would I trust anyone again? Bill echo'es similar thoughts later on in the game 'its not the infected that scare me, its the living' to quote.

Though maybe not intentional, as I reached the end of the game, it wasnt the infected I was afraid of having to fight next, it was the living. The infected are like animals in a sense, and they were predictable, the humans on the other hand were not.

So given all that info and all that he's seen, is humanity worth saving? is it worth sacrificing an innocent girl to save that? the other uninfected turned on each other as fast as the infected.

So now I go back to the ending, where Joel lies to Ellie, and kills Madeline (not sure if that was her name, I forget).

Firstly neither Ellie or Joel knew that to try to find this cure, Ellie would have to die. Had they gone ahead with it, Ellie never would have known, she would simply never have woken up.

But at the end Joel could have told her the truth, he could have said to her 'they MAY be able to find a cure, but to do so you would die'. It was already heavily suggested that had Ellie had that information, she would still be willing to sacrifice herself for that POSSIBLE outcome. When Ellie told the story of how she got infected, at the end my first thought was, she thought she was dead, she had already accepted it. She waited with her friend who she essentially watched die, expecting to do so with her.

Caps on some key words there because there was no garauntee it would work. There's no garauntee Ellie's sacrifice would have led to a cure.

Now going past that, speaking theoretically had Joel told her the truth, its safe to assume she would be willing to give up her own life to try and find a cure. Should a young girl have that choice? is she capable of making it? even today and in certain countries the 'right to die' law varies. Now going slightly to more realism, which I dont want to delve into much, in the UK a person cant simply decide to kill themselves, theres laws against it. Why, and are they right, thats a whole new argument which again, I dont want to get into.

But should a young girl be able to make that choice given the pressure she is under to do what she thinks is right? I guess that comes down to opinion.

But Joel takes away that choice, the doubt she may have had or desire she may have to sacrifice herself for the greater good (for lack of a better term).

Given how quick the fireflies were willing to sacrifice a young girl for the chance of a cure, again are those people worth saving? if I ask myself, would I be willing to scarifice an innocent young child for a chance to save those who have repeatidly proven themselves to be willing to abandon their own civility for their own survival time and time again, would I do it? F*CK NO! would I let a child make that choice? F*CK NO again!

At the end of that (semi) rant, I guess my conclusion is I dont see a world, or people who deserve saving, they have only shown a desire of self preservation, and abandoned any humanity they had to strive for that one goal. Even more so when the cost is the life of one young innocent girl who did no wrong, and there only too quick to be willing to sacrifice for their own goals. Would I let that girl make that decision herself when I knew what the likely answer would be? no, is that morally right to take someone else's own judgement from them.... that I dont know the answer too

But one last thing to consider, would you let a young girl make that choice when you already know she has seen how humanity has turned on itself? after she killed David she became so closed off and distant after as if she had lost all that innocence and belief she one had. She had already accepted death and was ready for it, which she thought was coming after she had been bitten and experienced the loss of her best friend who she watched die and was expecting to die with her. Would you let someone who has seen and experienced all that i a short space of time, make a decision like that?

That's what I like about the ending. Joel rescues Ellie because the Fireflies didn't give Ellie a choice, but at the same time, he also doesn't give her one, and continues to lie about. In part, it's obvious that he's doing it to protect her, but I also think it is for himself (she has become the new thing for him that is worth fighting for in the world). The sad part is that Ellie seemingly sees through his lies and you don't know how she ends up feeling about it, which ultimately makes the ending powerful.