That's not self-defense, not as it is commonly defined. Self-defense only applies when you are under threat of imminent bodily harm. By the time anyone knows that a nuclear bomb will bring imminent death, striking at the people who sent it does nothing. If you have an enemy that you're certain wants to kill you and has a known disposition to violence, it's not self-defense to go out and kill them. Substituting fundamentalist theists as the "them" doesn't change the equation.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.
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.'