Big Boss is pretty much the posterchild for Chaotic Neutral, dude. The fates of people, countries, and even the world as a whole are completely meaningless to him, but he's never actively malicious towards any of them.
All he cares about is HIS objective, which is fulfilling the last wishes of his dead mentor. If he has to kill people or start an endless war to do that, then too bad, but he's not going to just give up to avoid hurting people.
On the other hand, he stops a nuclear war from breaking out a couple of times just because he happens to be in the area at the time, even though the aftermath would likely turn the entire world into his dream; a place where soldiers will always be useful.