Tsuru. I find it hard to believe Sword is a rogue organization, especially if it is bigger than currently known. Such a thing will need resources, and given that at least one member is an active marine while the other is reporting to him, they can't just run around and do as they like since they still have other obligations as marines. So I believe either Tsuru or Akainu, or both, came up with the idea, Tsuru who has being hailed as a master tactician and is very knowledgeable, works as the director, kinda like Spandam with CP9 and reports back to Akainu.