Will Pepe be punished after stepping on Messi in the King's Cup?

Yes, Barcelona should appeal, and UEFA will give him a red card or a ban. There is also Coentrao's deliberate act of crushing Messi's head, and UEFA will also impose additional punishment on him, which may be heavier than Pepe's punishment. Their intentional fouls are evidenced by videos, and they only need to appeal for punishment.