Yeah I had a similar thing happen. The destroyed clans tend to resurface more often in territories surrounded by ronin, that are away from you or from troops. The best counter is to keep lots a few troops around to garison your territories, use your shinobi around, lower your tax rate, and build buildingss and improve farm land even if you don't need them for a miltary purpose or economic one I've noticed that they help keep your people happy. Just increaseing farm production and building a castle in one area I noticed caused one territory in a game I played to stopy having a revolting every 2 seasons.
To prevent religious revolts buid both Temples and Churches, if you do a balanced job of supporting both religions your chance of a religious revolt is less. A Temple abd Church in the same province works great.
finally keep an eye on your tax display as it shows you what the loyalty ratting for diffrent areas are, you can use that to figure what area's you need to make more loyal.
Finally take your time in advancing so not to extend your self. You don't want to take a territory, have it revolte or lose it to ronin or another clan just cause you over extending your self.