Metal Gear Solid V: Ground Zeroes by PatrickBrown

The original games gave no options for non-lethal playthroughs, it wasn't until the fourth entry that the tranq gun even became a thing.

Not to mention Big Boss and Snake are both sort of Blood Knight characters, part of their motivation was that while they suffered from it fighting was all they knew or wanted to do.

For Snake the tranq gun made sense, he wanted to keep fighting but didn't like the idea of losing his humanity.

But Big Boss, after killing the Boss and finding out the truth became disillusioned and depressed. He lost all reason to be loyal to anyone, and in essence lost his reason to maintain any semblance of humanity.

So Big Boss' story reason for using non-lethal techniques isn't a matter of morality but pragmatism. He spares soldiers who are worth sparing, a good example being Kaz himself.

Remember, there's a reason Big Boss is the bad guy in the original games. He values his allies, his men, they're true companions to him. But Big Boss doesn't see human life itself as inherently valuable.

Remember, Metal Gear is a series that holds the characters as well as the player's morality in the equation. Metal Gear Solid made a specific point about your wanton killing, the player and Snake are considered the same thing. Therefor Snake's character must contain within it both the player's capacity for mercy and wanton killing at the same time.

Play Snake or Big Boss however you want, their characters are written as such that your behavior as the player is never out of character for them.