I did it non-lethal on Give Me Deus Ex difficulty. It's hard but doable.
You have to carry a tonne of energy food, the taser and the tranq gun. Basically when the cut scene finishes whack on the cloak and run round like a maniac tasering everyone. The videos online suggest using takedowns but they waste energy which kills the cloak then you get filled with lead. Then before the bot shows up pick up everyone on ground level and lob them into the corners of the map. Then EMP the bot as soon as it spawns. Mop up the guys in the towers using the tranq gun. Bob's your mother's brother.
The hardest bit is clearing the bodies quick enough before destroying the bot, if you leave the bot too long Malik dies.
I found the thing that takes the most work is preventing the barrels on the top right from spontaneously exploding and killing that one guy, and the same with the mech when it explodes.
Following the many uploaded videos, I found it easiest to run up the right hand side (on the shipping crate, to the walkway) -> stunning the first guy. Then there's one behind a pillar and one comes up the stairs - either double takedown or 1 stun 1 takedown depending on their position. Get down to the bottom and stun the heavy(ies)/troops at the back. The mech should now be active. Go back under the same walkway you came down and stun/takedown that one (two?) guy.
Unfortunately I had one heavy run round the back of the helicopter each time on several attempts so had to run behind to stun him.
EMP the mech, making sure there is enough distance from the knocked out troops and the one on the left side ground (behind the mech) - this guy was a pain; killed by the mech explosion several times from being too near.
Anyway after that guy is stunned the two snipers are easy (stun/takedown).
The challenge is deciding on a sequence and carrying it out as efficiently as possible.