Those are more connected than you might think. But one piece at a time.
Here's the quote from The End of Faith regarding a nuclear first strike that's so often bandied about. The bolding is Harris' not mine. I'm putting it here in it's entirety not to put up an argument by text wall, but to highlight how important the nuance of this position is.
It should be of particular concern to us that the beliefs of Muslims pose a special problem for nuclear deterrence. There is little possibility of our having a cold war with an Islamist regime armed with long-range nuclear weapons. A cold war requires that the parties be mutually deterred by the threat of death. Notions of martyrdom and jihad run roughshod over the logic that allowed the United States and the Soviet Union to pass half a century perched, more or less stably, on the brink of Armageddon. What will we do if an Islamist regime, which grows dewy-eyed at the mere mention of paradise, ever acquires long-range nuclear weaponry? If history is any guide, we will not be sure about where the offending warheads are or what their state of readiness is, and so we will be unable to rely on targeted, conventional weapons to destroy them. In such a situation, the only thing likely to ensure our survival may be a nuclear first strike of our own. Needless to say, this would be an unthinkable crime—as it would kill tens of millions of innocent civilians in a single day—but it may be the only course of action available to us, given what Islamists believe. How would such an unconscionable act of self-defense be perceived by the rest of the Muslim world? It would likely be seen as the first incursion of a genocidal crusade. The horrible irony here is that seeing could make it so: this very perception could plunge us into a state of hot war with any Muslim state that had the capacity to pose a nuclear threat of its own. All of this is perfectly insane, of course: I have just described a plausible scenario in which much of the world’s population could be annihilated on account of religious ideas that belong on the same shelf with Batman, the philosopher’s stone, and unicorns. That it would be a horrible absurdity for so many of us to die for the sake of myth does not mean, however, that it could not happen. Indeed, given the immunity to all reasonable intrusions that faith enjoys in our discourse, a catastrophe of this sort seems increasingly likely. We must come to terms with the possibility that men who are every bit as zealous to die as the nineteen hijackers may one day get their hands on long-range nuclear weaponry. The Muslim world in particular must anticipate this possibility and find some way to prevent it. Given the steady proliferation of technology, it is safe to say that time is not on our side.
The threat must not be a Muslim country, but an Islamist country. A radically, suicidally, Islamist country. Harris himself admits the craziness of his scenario. But he's also pointing out the craziness of the people responsible for radical acts, the commonalities of their beliefs and behaviors, and the idea that the same guy who is cool with ramming a plane into a skyscraper is probably okay firing a nuke suicidally. Extremis meet extremis.
Harris is about first principles largely. And if you start with the principle that murder in self defense in some instances (Not all) instances is defensible, even if it's only defensible as part of a cycle of mutually assured destruction, you can arrive at the argument in favor of a first strike in a cold war scenario, and an enemy with a known disposition. That belief is not incompatible with a desire to be more mindful, less impulsive, etc ad nauseum whatever benefits you believe meditation does or does not have.
I don't believe I can convince you of the power of a radical, sincere, bone deep held religious belief. I'm going to try to build it up the way it was built up to me. To arrive at the point of 'Homosexuals are moral deviants who need to be ostracized or purged.' you have to start with a lot of other far less radical assumptions/beliefs. First you start with Biblical inerrancy. Then you add on Biblical Literalism. Then you add the idea that ALL humans deserve violent, painful death and eternal punishment, but YOU are one of Gods elect, saved from fire. When the 'other' in an us vs them dynamic is sub-human in a very concrete and literal way, it allows for further slips of what we might call 'rational thought.'
The church I grew up in preached that those who lived lives in 'sin' deserved death, disfigurement, and every form of horrible fortune. I heard that at least once a week, in some form or another, for the majority of my formative years. Us lucky few True Christians did too, but because we were in the right church, we were saved. Notice, not, a church, not our church, but the Right church. Sin in this instance being defined as any behavior outside of the strictures of the Old Testament they chose to obey. Don't pierce your ears or wear makeup, but cigarettes aren't in the Bible. Don't watch TV, but if you want to eat yourself to death we are happy to enable that behavior, gluttony is forgivable So long as you come to church and get weepy about it every so often in front of your peers. I don't know if you know what a shame culture really is until you've seen grown adults force other grown adults to sob regularly as a pro-social behavior. We were the chosen people of God, watched over and protected in every moment of our everyday lives. I was taught that the reason why we didn't treat gay people the way they did in the old testament was because we were nicer. 'These people are sick, we shouldn't kill them because they are sick. (Never mind that's illegal), they should be saved.' Not 'This is a barbaric and outdated part of a historical document that's been important to a lot of people for a long time.' but 'We need to feel superior to our ancestors as well as everybody else, also it's illegal.'
These are beliefs I genuinely held at one point in my lifetime. Knowing what you know of me now, how do you think I regard those opinions? This church still exists. My best friend from childhood left it about the same time I did, but got a girl pregnant who still attended, and married back in. The difference, I've been told, between the old guard of this church, and the new young adults my age (Who already have 2+ children) is that the new generation keeps their homophobia, racism, and general religious bigotry quieter to outsiders. Some of them are genuinely more moderate than their peers, but keep those opinions quiet because 'tolerance' in the sense that you understand it is not a virtue to these people.
This turned into a much bigger argument than I intended. I posted this wanting to talk about meditation. Sam Harris wanted to talk about how we can divorce spirituality and spiritual pursuits and virtue from organized religion, because of all of the anti-social stuff attached to pretty much every religious institution as matter of inertia. I won't say his stuff isn't controversial. If it wasn't nobody would be interested in it. I would like to address other topics eventually.