I had a new baby king take over after his father was assassinated and several faction independence rebellions followed. During one rebellion both the Sunni and Shia declared Jihad on me (one for Jerusalem, one for Andalusia). I defeated the rebellion and then won the Jerusalem jihad, and while waiting for the counter to tick up to 100% for the other Jihad I noticed that although there was a strong independence faction they didn't declare war. At one point it was at over 120%, and they surely had enough support to attack. I believe the reason they didn't attack was because of the penalty they get for declaring war on somebody defending against infidels. I allowed the Muslims to capture one holding and if I keep it like this then there will be no more rebellions. It seems a little gamey, but other than that I can't see any reason to recapture the holding and win the war, at least until I've got a decent long reign bonus.
On another note, the rebellion wasn't defeated, I ended it with a white-peace, but the leader of the faction was still imprisoned. I then revoked his duchy and banished him (his heir was also the heir to Scotland, and keeping him in place would have meant losing the rich duchy of Sicily). It doesn't seem right that a white peace should have sent him to prison.
On another note, the rebellion wasn't defeated, I ended it with a white-peace, but the leader of the faction was still imprisoned. I then revoked his duchy and banished him (his heir was also the heir to Scotland, and keeping him in place would have meant losing the rich duchy of Sicily). It doesn't seem right that a white peace should have sent him to prison.