i agree with you, i don't have an explanation that is any better than yours. however i feel that proves the point enough to say it was at the very least stupid and didn't make a whole lot of sense. just think about this, a scenario of a microwave corridor before shutting down a world controlling AI and an after death message where naomi apologizes because she KNEW they would shut it down, much like ocelot KNEW snake would shut it down too? this is beyond ridiculous. this goes along with my whole theme of they did whatever they want with very little justification. also, it has an ending that no one would ever predict in a million years (ending sequence revolves around meryl and johnny getting married). my general complaint from that comment is that the story feels very lazy, and i think that my original point still stands that it isn't very clear why snake HAD to go (again, snake sat down the entire time doing nothing).
i got an EMO vibe from snake when he kept saying HEH I DONT HAVE A FUTURE. both snake and raiden are arguing over who should MAYBE DIE??? when there are a shitload of frog soldiers around them was idiotic. i was 100% sure snake was not going to die given the theme of the game was SNAKE FEELS MORE PAIN. look at him on the boat when he saved big mama from the fire too, only for her to die shortly after anyway. this is idiotic because she literally leaped in the fire too. man, i have so many issues with stuff they did in the story i really wouldn't waste the time to list them all.
in any case, you will be hard pressed to find anyone (even kojima himself) who could adequetly defend all the decisions made in this game. as in, how it makes sense even in the game world itself. many people would agree this game is a fan service, and this is already a bad sign. i don't know what you thought of the story, but i can say with a lot of confidence the story has a tremendous amount of flaws and a lot of it is due to appealing to fans and trying to close out the series. just think the MGS series answered 95% of questions in one game, when it was a series that spanned several games and consoles.