Unfortunately, there's no real way to make that happen, so instead, we'll keep doing what we do now: patrolling the front page and killing stories that present too many opportunities for comments like yours.
It's too bad, that comment! Usually, when I read a comment like this, I click through the profile looking for other terrible comments to flag, and usually when I do that, I end up wading through a cistern of crap and malevolence. Not in your case! Anybody who can write comments that start with "I work for an EMR provider and..." has something to contribute to the site. Why muddy those contributions with stuff like this?
Seems like banning / downmodding users should work just fine, instead of killing off the whole story.
It's also true that all stories are an opportunity for snark. But it's not true that all kinds of snark are equally toxic. The kinds of snark that fill up threads like this are particularly bad.
What is not widely known is just how fragmented and unbelievably complex that U.S.-Pakistani relationship actually is, not to mention the relationships of various groups within Pakistan, which is why the idea that "oh, the CIA just runs Pakistan" is so devoid in substance. Pakistan doesn't even run Pakistan, let alone any CIA puppet-masters.