The best way to get an S rating in this mission is to be fast without ever being detected(or to be SUPER-FAST with being detected.) Equip the Sneaking Suit as well as a nonlethal sniper rifle. When aiming at armored soldiers, fire at the parts of their bodies that a dart can reasonably be expected to penetrate. Even if their heads and torsos are covered in garb that looks as if it might stop anything short of a direct meteor strike, further scrutiny will usually reveal legs clad in nothing more than cloth, or exposed arms. Fire multiple darts in succession if you can't land a headshot. Silence only the soldiers directly in your path, and be sure to skip the closing cutscenes to save a lot of time.
