I get what they mean, I simply don't see how that is or how the show treats it that way so it seems like it's a complaint that the kids' issues play a role at all, franlly you can't really dissect human nature from large scale logistics and it's not that much of a "two sides" issue as most of what would wipe out "the world" would also kill our protagonists it's not really a juxtaposition as much as a situation that's sorta bleak and hopeless in both the macro and microcosm level.
Our protagonist's aren't really "separate" from the mass of the people - they're examples for people who might get wiped out & have to fight against it.
You could also show the story from the perspective of some random NERV employee or somene who just contributes tax money as far as that is concerned but let's not kid ourselves they'll point the camera where the action is.
- indeed the certainty that Misato & the others have that the kids very much aren't morally more important is essential to the drama & themes of the show at least as I perceive it: Ritsuko's polite enough but is ultimately detached from the "human ressources"; Fuyu sorta halfassedly voices ethical quals but is essentially the same, Misato is all conflicted both because of her personality & just because she works more closely with the kids, and Gendo who's more "morally flexible" to begin with is in this weird halfway space where he sees no contradiction between making Shinji & Rei fight for their lives one day and interacting with them normally (or as close to that as he gets but that's a different issue) the next day & probably thinks the utopia of instrumentality will make up for everything.
A smaller wrong may be justified but that doesn't make it a good, the cost isn't nothing and it's gonna be hard for someone like Misato to go through with it - Not taking that nto account would simply be unrealistic. You can't just ignore the human factor simply because it would make sense - what more, a scenario where you expect it not to come in to play is what wouldn't make sense. It may be justified but it's still not right, there just isn't a good choice & that's the story.
& the whole thing really should be analyzed on the level of the adults (Misato & co) & how they act because the kid's don't really understand the big picture (except maybe Rei but she's indoctrinated into Gendo's view of things at first), nor would it be surprising for them not to have that maturity at their age. - that's part of the complication.
I mean to some extent you end up pursuing this to the fundamentals of how morality works & the different opinions peole have of it & the reality is that neither the fully utilitarian nor the fully kantian view should just be swallowed without caveats b/c the world throws complex situations at us.