Joel lost his daughter at the start of the outbreak, and doesn't want the responsibility of escorting Ellie. Indeed, he tries to pass her off on his brother half way through their journey. This is where The Last Of Us really excels - the plotting and characterisation is simply sublime. Along the journey Joel grows to love Ellie and cannot give her up. So when the scientists reveal that the neccessary surgery will kill her, Joel kills them all and rescues her.
And so the first moral dilemma. Did Joel do the right thing? It's a tricky one. The scientists themselves surely thought they were in the right; killing one to save mankind is the ultimate in utilitarianism, and who can rationally disagree? And so was Joel wrong? I don't think so. Ellie never agreed to sacrifice herself, and there was no guarantee the scientists would even find a cure. And Joel didn't even really have a choice - he'd already lost one daughter, he wasn't going to sit back and lose another. A rational part of me argued, "Just look at the stats - one death to save millions..." whilst the emotional part of me punched the air when Joel rescued her. People aren't just statistics when you know and love them.
The second moral dilemma, The Lie, came when Ellie awoke. Joel told her the scientists had worked with hundreds of immune people, that nothing had worked and so they'd given up looking for a cure. Even when she displayed signs of Survivors Guilt Joel swore he was telling the truth. Why did he lie? Because he was scared of losing her. He was scared she'd choose to go back and give up her life, and so he took the decision away from her. It was selfish of him, and lacked the poetic scenes of self-sacrifice I'd been expecting, but it was more real. Joel is a survivor, and he decided he couldn't survive without her. It's the only thing he could do.
And hey, hopefully it'll mean a sequel.