I choked a quest NPC - do I need to do the whole level again or can I do something to wake her up?
You immediately get a game over if you KO or kill anyone that is actually required. If the game let you kill them, they're not story-relevant anymore; this happens to a few NPCs you can't kill in earlier chapters at certain points in the game. Just continue the level as normal, only reload if you're doing a no kills/unseen run and you messed up your 'streak'.
Note that non-essential sidequest NPCs can be KO'd or killed without a game over. Depending on the character this may not matter at all or it may make the quest impossible. So at worst it's possible to lock yourself out of some bone charms/relics/money. If you choked the Witch she'll actually just warp away and be hostile to you.
Note that there is absolutely no way to wake up a KO'd character. They will stay unconscious until the level is reloaded (via a save before the KO or restart) or until rats/water/you kill them. (KO'd characters can also despawn, but if they despawn while alive they count as alive as far as the game cares)