originally posted by Kindred
You're allowed to kill the bosses. It states that explicitly in the achievement description. Note for the final boss:
You're not allowed to kill the Hyron drones (the women in the pods) or the crazed Belltower soldiers so be sure to have a supply of non-lethal weapons before you go in. Zhao herself you can kill and still get the Pacifist achievement - I used a rocket launcher.
As for the fight to save Malik, I managed it without killing anyone (on my second playthrough using prior knowledge) by having a heap of healing supplies, a couple of gas grenades, and by drawing fire from the soldiers. You might want to prioritize the two guys with heavy rifles first, and remember to always have an EMP grenade for that freaking box bot.
Actually I think the Hyron drones are counted as part of the boss battle. I used the code Darrow gave me to shut down them down, which I'm sure cuts off their life support, and I still got the Pacifist achievement.