A town cannot rebel to the faction that controls it. If the faction owning the faction is the faction that the town will rebel to then the town will rebel to the rebel 100% of the time.

When public order shots up it is simply the AI lowering taxes and such.

Because of possible bonuses of taxes, garrisons, and cheaply built buildings it is almost impossible to use spies to cause a city to rebel when they are anywhere near the faction's capital. The only practical use of this tactic would be for someone trying to make AS's far east provinces rebel or such.

Also, keep in mind that adding more spies doesn't always help. There is a cap on how much unrest spies can cause and two or three spies will usually reach this cap.