The Iodine triggers the infected cells to start apoptosis - preprogrammed cell death, so that new cells can take their place.
The redness and somewhat murky (grey/black) skin you describe is likely the leftovers after the Iodine did its' work on the upper layers of the facial skin.
Since you mention you applied the Lugol's because of herpes blisters, I think vitamin A is important in your case (antiviral).
A home-made salve with a base of coconut oil should help speed healing by providing building material and protection while your sub-dermis (underlayers of skin) are producing new cells.
No, defects in the skin are not necessarily permanent, especially after applying iodine. You solution (mix) that you painted on the skin may have been more powerful than your capacity for generating new skin cells in that area (the face).
A gentle salt scrub (a good basic one is lemon juice, honey and fine salt) can help remove the scarring- just avoid rubbing so much that it's painful.
Wombat makes some very good Iodine face creams that I suspect give a very different result- you can try researching her methods and mixes to prevent discoloration when you apply iodine in the future.
If you have red palm oil, vitamin E oil, or spicy-tasting olive oil (if it doesn't taste sharp it is likely an adulterated oil, buttery flavor is a sign of a high omega-6 content. The sharp flavor is the olive essential oils, which makes up a good deal of it's healthy qualities.), they are also very refreshing for the skin. I'd apply several times throughout the day to speed healing.
It's possible that the dark parts of the skin are places where the Lugol's has not been entirely absorbed. Lemon juice (or just laying lemon slices on the skin) or, if you have vitamin C crystals, vitamin C in a few drops of water can help remove the darkness (vitamin C clarifies Lugol's solution from brown to clear).