I finished with clean hands on very hard. By the end, what I had maxxed out (if you're OK with Merchant of Disorder instead of Mostly Flesh and Steel achievement)
Blink 2
Agility 2
Dark Vision 2
Possession 2
Bend Time 2
I threw the rest into Vitality, but that's just for craps and giggles.... don't need anything else for non-lethal, imho.
Invest in getting Boot Stealth 1 and 2 as soon as you find the schematics. Also Mask Optics for more precise shots, Crossbow Range and MOST IMPORTANTLY,
(as in, get as soon as you can) Combat Sleeping Darts.
If you get lucky and get the Strong Arms bone charm... hug it, equip it right away, love it forever and ever. Best charm in the game for ANY playthrough.... but especially
non-lethal. And there's another one, Fleet Fighter, that lets you move at full speed with weapons drawn... which is also very handy.
And yes,
Spoiler the end differs depending on you chaos level at the end of the game.