The ending where 47 dies at the end of the game (on Requiem) is not the game's real ending. What you need to do to achieve the real ending is to move the left joystick (it may be mouse or keypad on PC) back and forth (during the credits) until a surprise occurs.

Note that you will need to quickly eliminate all the witnesses in the level. All the guards in the main chapel carry weapons so you should take them out first. Good luck!