I've had multiple games where it hasn't happened. The event window has popped up but the split didn't happen (yes, Catalonia completely Republican owned at the time). So, there are some circumstances under which it doesn't.
Regardless, I think it would be better if some mechanics were in place to allow a centrist republic to delay it longer so that the full-blown conflict only comes in ahistorically as a tie-breaker if the Republic outlasts its historical lifespan. Maybe add a few factors - being on the back foot delays the end of the mission - giving them autonomous status and then releasing them as an integrated puppet or colonial nation hurts your war effort and strengthens the rebellion but delays it significantly - so on and so forth. That way you aren't just eliminating them as a factor from a historical run, but you aren't really going outside the bounds of history and at the same time you're making them a more interactive and strategic gameplay element.