There is a way to kill The End before you even fight him. If you swim to a hiding place across from the Ponizovje Warehouse, you are in a perfect spot to snipe him. If you do kill him this way, Zero and the other support team members will congratulate you for killing him, although Snake will express disappointment in killing him in the manner that he did, as was hoping that he'd actually face him in battle. If you do this in the HD Collection, you will get an achievement called "The Early End."