Depriving her of her make-up? XD

Give her to Disney and make her live with whatever odd incarnation they reimagine her as.

Every bad punishment it would be good to her, concideranding that she likes feeling despair, so probably just jail forever.

Honestly, as horrible and evil as Junko is, she's still human, there has to be a limit, a way to break her view of despair. Then, it's up for you, what would you do to a non-emotional masochist Junko?

Having s*x with her!