Morathi is the only special character allowed in the Cult of Slaanesh, and if the army is led by her then she will always be the army general.
In a Cult of Slaanesh army, Morathi's special rule, Beloved of Khaine, is removed. In addition, she has the Mark of Slaanesh (at no additional cost).
Her High Sorceress special rule is slightly changed Morathi may choose four spells at the start of the game instead of rolling for them. She may choose from Dark Magic and/or from the Lore of Slaanesh.