Yeah, non-lethal can still be lethal if you have bonus damage since your weapon damage will be prevented from being lethal and leave them at 1hp... Then your bonus damage will apply and just kill them.

Would be helpful to have a Sneak Attack style "Knock Unconscious" ability that can be used in lieu of a regular attack (Like whatshisface uses against Isobel) that could provide the effect of not allowing any portion of the attack to cause lethal damage (Including stuff like Cull the Weak Illithid power). Given there are benefits to knocking certain characters out (Often, it's the ability to steal equipped items without permanently removing the character from the game)

That said, you don't need to knock out the Hag. If she starts her turn at like 30-40% health, she'll go into dialogue with you.