I suppose you could always make the consequences of losing a Civil War so damaging that you would always want to avoid it. I understand why Paradox designed it the way it is, but it seems to me that it restricts your own liberty to play, ehen Paradox games are known to grant the player the liberty to play as he likes. In other games, if you screw up, you'll always have a second chance to rebuild (unless you have been completely annexed). Sure, not everybody has the patience to do so, but it can feel very rewarding if you achieve it.
Constantly, nervously watching the Civil War countdown does not sound like a fun way to play.