When Malloy reminds Snake of what appears to be the list of rules for living in the New Moral America, one of them is "no foul language." Malloy personally breaks this rule at least once, and most notably the president himself takes the Lord's name in vain - something you'd think a fascist theocrat who criminalized atheism would take very seriously... were itsomeone elsedoing it.
Why does Snake insist on using Hershe's original name (Carjack) despite repeated demands that he stop? Because as far as he's concerned, the one who betrayed him in Cleveland (a betrayal he's clearly bitter about) was Carjack Malone, not Hershe Las Palmas.
Sure, Snake shuts down Earth as a badass act to say screw you to the president, but with this one act, Snake possibly kills millions of people. Picture this: where are electronics most vital? Hospitals where people are in ICU or getting treated, as well other stuff to help people like pacemakers or iron lungs. What the fucking hell, Snake?
"Millions" is being fairly conservative- billions would likely perish without the electricity needed to run water treatment plants, sustain modern agriculture, produce and distribute vaccines or simply move anything at a pace faster than an a horse.
Hell, forget about hospitals and pacemakers. Imagine the cooling systems of every freakin' nuclear power plant on this planet failing simultaneously, with absolutely no chance of emergency cooling whatsoever. Imagine Fukushima times… hundreds?
He could also be aware of the consequences but genuinely be that dark, making him either an extremely sinister Sociopathic Hero or a Villain Protagonist who finally shows his true colors, but just happened to be fighting other villains before.
It's still a ridiculously extreme move, given that like at least 80% of the world he shut down had nothing to do with the plot.
If there was some way he could have shut down both the US and The Shining Path, and spared innocents at the same time, he may have gone with that. Wasn't an option, unfortunately.
Maybe less than half of that. The Shining Path is stated to be as much Mexican as it is Middle Eastern(Mexico Called; They Want Texas Back) and if they have the resources to launch a trans-Atlantic invasion via Miami they're not worried about getting hit by the UK, China or Russia, either because the Path conquered them or because they're part of the Path. And if that much of the world is under the control of fundies or terrorists, the hanger-ons are next once one side falls. Snake saved them, too.
On a more immediate level, the few half-decent people Snake, himself, encountered during the course of the film are screwed also. Sure, the President can't have his daughter executed in the chair anymore, but all those men who'd been taking orders for him still have their guns: either he, or whichever one of them deposes him for screwing up, can still kill her - or worse - in retribution for putting them in this situation in the first place. Likewise, the surviving Shining Path members in L.A. are used to operating on minimal or no technological resources, and can still hunt down anyone who assisted Snake in his operation. Finally, Snake himself (or at least his hologram) just appeared on the last ever global TV broadcast, meaning there's nowhere in the world he can go where people won't recognize him as the asshole who just knocked civilization back to The Dung Ages: his plan to "disappear" will work, but most likely only by having him "disappear" into an unmarked grave, soon as anyone with a still-functional weapon and a grudge can draw bead on him.
In 1997, the government was corrupt and run by a man who didn't show much appreciation for the people who saved his skin, and crimes rates have gotten so bad the government abandoned its largest city and turned it into a penal colony. By 2013, America is a theocratic hellhole run by a maniac with a God complex who wants to bring about the end times himself. Snake has witnessed an America that has really fallen far from its title of "The Land of the Free." The revolutionaries who oppose this madman are just power-hungry wannabe dictators who would be as bad or worse. Even if Snake could leave decayed America, there isn't any side he could join that is objectively good or wouldn't try to screw him over.
On a personal level, he's experienced and witnessed a whole lot crap in his life: he's been betrayed by many people, and he's seen so many decent people undeservedly die. In this movie, a girl he genuinely cared about was shot and killed before his eyes, and a deranged surgeon nearly took his remaining eye.
As horrible as Snake's decision, the world hasn't given him a single thing to hope for. He thinks putting it out of its misery would be better. The above entry mentions that the world will hunt him down for his actions, but after all the horrors he's endured, he probably Stopped Caring long ago and would rather die than continue to live in this trainwreck of a world anymore.
