you better you better you bet

Hell, real governments have been able to use these methods--anyone remember when The War on Terror "ended"?--even when they weren't literally controlling both sides like Palpatine is. Dude, you have the tools! You can keep these CIS guys (teehee) in the fight long enough with intel, draw out their inevitable demise for plenty more years. The more of a dictatorship the Republic becomes, the more enemies they're going to make without even forcing anyone's hand--and eventually those groups of real rebels will mingle with the CIS, at least in the imaginations of the citizens. Yeah, the CIS leaders also do know a little bit too much for comfort, and will outlive their usefulness, but when it's time to kill them off, it should be when there are enough others to take their place to ensure plenty more wars. Ideally (for Palpatine) the rebellious factions should become so mushed together and indistinguishable that most people don't even register when the last member of the little CIS leadership council dies; it's in the holo-papers but nobody even remembers where one thing began and another thing ended and the few who remember the name may have trouble remembering which faction he was with. Everything's melted together into a big, amorphous, faceless Enemy.

Then you can cook up your constituency so slowly that they don't realize they're boiling until it's too late. Make them forget about the time before there was a Palpatine, so they never dream of a time after there's a Palpatine. He simply is the Emperor, and the more you refer to him by a title like that, the less possible it seems to remove him from power.