i think when ussop said that she needed permission from the captain of the ship to leave, she really did want to return to being with the luffy crew

she went back to the CP9 guys because she promised to go with them, in return they will not hurt the straw hat pirates
Robin still probably has doubts about the power of Luffy and co., she probably thinks they dont stand a chance against the government, still she is thinking about the safety of the pirates