This could be a bug or a feature but whenever I capture a pirate base and make it my own the pirate leader remains in residence and his faction continues to raid my stations and demand protection payments. I cannot move him or assassinate him he just keeps on living in my base and leading his faction.

Same issue here for the last several updates including the new 1.0.4.1 beta. I capture the base and the pirate leader stays in residence and his faction continues to exist and raid me with the occasional offer of protection.