While Seth was fighting a mental battle against the conjoint ability cast by the Illusive Ethereal Goddess and the spirit inside of her orb, on the outside world his body was temporarily unprotected.
He still had an absurd level of toughness, brought by the enhancements from the Seed of Tyranny, but the Mana circulating inside of his veins and his ability to freely move, had been prejudiced.
Fully knowing about what would happen to the individual subjected to her soul techniques, the Illusive Ethereal Goddess had taken that into account, to previously order her puppets to assault Seth as she attacked him.
She was also temporarily paralyzed, since it was not an easy task to invade the mind of someone who was at their level of power, and even with the help of her weapon's spirit, she had to be fully concentrated to accomplish that task. That's why she sent her minions to do the dirty job, instead of one of her clones.