As someone who finished my first play though on PS4, the ending was something really special. It's genuinely rare in games to show morality in that kind of grey.
Under no normal circumstances could a 14 year old be legally allowed to consent to experimental surgery that would kill them. It's never made clear if she's given informed consent to the operation anyway, but what traumatised person, especially a 14 year old (who we later find out is semi-suicidal) is going to be able to make that choice? Especially if they're being coerced by adults telling them it's the only hope for mankind or similar.
Joel's actions, as have been said, are brutal, stupid & savage, but very, very human. By this point he clearly sees Ellie as Sarah, and the situation he's presented with is the government killing another little girl.
Another poster up thread said it - during the epilogue I felt myself distancing from Joel, and by the time I was controlling Ellie everything he said felt wrong & forced and the lies seemed worse than when he'd lied before.
But goddamn - what an amazing game. Presentation, gameplay, acting , sound design. None of it ever felt cheap - cheesy maybe, but not cheap - and some genuinely chilling & terrfying moments.
The funniest thing is I never felt scared by the Infected...I did every single time I met a human though. Winter, followed by the very beginning of Spring until they go down the stairs after the giraffes, is one of the best narrative sequences in a game I've come across.
_/¯
