First thing you have to do: make sure there's actually a separatist. I'll often feign a Separatist if I'm behind than everyone else, so as to force them dump resources into avoiding rebellion. Chances are, he won't pull the trigger if he's actually feigning a Separatist - except if he prefers the "let's lose the game altogether" scenario. In the latter case, you have to be prepared for that in every single game!
im curious to know some advices to stop the separatist player.
Once your group in play identifies the separatist player. How do you manage to prevent his massive rebellions?