I do believe that the plan of the WG was that not all of CP0 were to leave Egghead after they were to murder Vegapunk in the first place. I see Stussy having additional orders and making sure the assessination was running smoothly as it should (It did not since Luffy and the crew has arrived on the island - so Stussy informed Akainu about this - she is with the navy, still and will stab egapunk in the back when the situation arises.)