Non-lethal runs are pretty manageable without target analysis, which isnt even available after the 2.0 patch anyway. The easiest approach is grabbing some blunt weapons or using your fists since they're non-lethal by default, and gorilla arms work great if you've got the cash. System collapse quickhack is super reliable for takedowns, while regular stealth knockouts work perfectly fine too. Finding a pax weapon mod lets you convert most guns which is neat, and theres always skippy in puppy-loving mode if you want something special.

Just watch out cause enemies can still die if you're not careful, especially from environmental stuff or hitting them too many times when they're down. Quickhacks like short circuit need precise damage control, or they might accidentally finish someone off. Scripted fights sometimes force lethal outcomes but dont worry too much about those since they're part of the story anyway.