It's not lethal weaponry Sakurai is opposed to. It's "realistic" weaponry. Explosions and weapons derived from such are more commonly associated with cartoon violence, so weapons like rocket launchers and bombs are usually fair game. Realistic guns, ballistic firearms and shorthand blades however lean more towards "realistic violence", most likely because there's a bigger element of brutality associated with them. And I'm not the one who makes the rules on that; that's usually how the rating boards judges the level of violence in games. Sakurai employs a similar metric to keep the game's subsequent age rating in check.
And im saying its easy to come up with 4 specials, throws and normals without using realistic rifles or pistols. Having a combat knife doesn't seem to be an issue any more if Snake has one.