You can turn off Separatism in the custom game options. Having said that espionage is the key to controlling Separatism, just like the real world.
I like this separatism idea. Really nice to know about espionage helps with that.The problem is the AI if all of them sooner or later collapse there is no point to continue playing my curent game. Just surviving means 100% win.
So it looks like the only solution now is to turn it of (for those who like challenge).
What about barbarian civs? Should I turn them off too? I read about problems or bugs there.