Some Paradox games had similar mechanics and it sucked for me. You are developing your empire and plan strategies and everything and then suddenly you are punished by a lengthy campaign to reconquer your lands, and even if you are successful, you suffer a big setback compared to the competition. It's a good reason to ragequit because it's an almost random and brutal punishment.I kinda somewhat disagree with the Civil Wars not being good for Mount and Blade, but I can see why they could suck. If all that Civil Wars do is split your kingdom in half and you have to retake all of those keeps, then yeah that would suck.
However, if there is a system where you can crush the Civil War and all the keeps are just added back into your kingdom, it would be a nice addition to the game.
The gameplay problem is there is no gain from this, except being spared from another civil war for some time. Invent and counter-balance some gain with the punishment and you may get genuine gameplay out of this.