I don't think Xemnas (or possibly Saix) wanted anyone to know that the Organization was killing its own members, even if they were traitors. He just ships them off to CO, and a few unfortunate accidents later, all the loyal members would have come back. Notice how the loyal members were assigned to the Basement, where they wouldn't have been aware of the nasty details, and how no one in Days ever suspects Marluxia and Larxene were even traitors. It was a nearly perfect job. Too bad Saix wanted a few extra people dead...