The same way Cerberus isn't a part of the System's Alliance. they may use resources from it but they don't answer to it. Which makes them a rouge terrorist group.
But the people who make up S31, are from within the Federation. Sloan is a human, iirc from Earth. Why would the hundred of billions of people from the many Member worlds have to "answer to" the Federation?
You make the Federation sound like a police state.