Dude The Fireflies didn't even wake her up, the last thing Ellie remembers was fucking drowning and some random group was going to take an ice cream scooper to her brain to justify their bullshit.
Ellie can be pissed she was robbed of making a choice, but The Fireflies didn't even give her a choice, or Joel a choice. Nothing in Left Behind reinforces anything other than Riley's death causes her immense guilt. Saying that "letting Ellie choose suicide at the age of 14 while she is ripe with survivors guilt" is kinda fucking insane. Yea, Ellie is pissed, she has very valid reasons to be mad at Joel. That doesn't mean Joel's actions were in any way wrong. It's insane to have some random group filled with horrible people go, "Ok Joel, we're going to kill your daughter, you're going to fuck off, but you should be fine with it because she is super depressed and feeling insane survivors guilt (even though The Fireflies don't know this), so go home and fuck off or we will kill you", and thinking that Joel going "lol no" is somehow an unjustified response.
Your reading on Left Behind basically sounds
really insane if "knowing what she wants" translates to
assisted suicide at best and 1st degree murder of a juvenile by a bunch of desperate idiots at worst.
That's the critical flaw in Neil's interpretation, Joel didn't really have a choice or any say. They didn't let him talk to Ellie, see her, they put a 1911 to his skull and told him to pound sand. They 100% forced his hand and in effect had to "choose" for Ellie.
#FuckTheFireflies