Can I still get the Pacifist achievement if an NPC accidentally commits suicide?

Looking at the wiki page:

http://deusex.wikia.com/wiki/Pacifist

I think incompetent AI may affect the achievement. I would rather be safe than sorry and make a save just before the shooting starts and go stealthy to the elevator. If your going for the saving Malik achievement go back to the save you made earlier and use lethal weaponry.

Just to clarify, you don't actually have to save Malik to get the Pacifist achievement. So you can just run past all the guards and go into the elevator, without any risk of discounting the achievement.

But to your question, this does count against the pacifist achievement.