Does killing in the opening sequence count against the Pacifist achievement?
Solution 1:
According to this thread at Xbox360Achievements.org, kills in the opening sequence do count towards the achievement.
Since my original link died, the IGN Strategize on Deus Ex: Human Revolution also states that kills during the opening (pre-augmentation) sequence do count against the Pacifist achievement.
Solution 2:
You can't kill, but you can shoot the yellow gas-canisters in the vicinity of enemies, that will render them unconscious.