We know how a powerful hurricane is generated:
Tropical cyclones typically form over large bodies of relatively warm water. They derive their energy through the evaporation of water from the ocean surface, which ultimately recondenses into clouds and rain when moist air rises and cools to saturation. In most situations, water temperatures of at least 26.5 °C (79.7 °F) are needed down to a depth of at least 50 m (160 ft); waters of this temperature cause the overlying atmosphere to be unstable enough to sustain convection and thunderstorms. Another factor is rapid cooling with height, which allows the release of the heat of condensation that powers a tropical cyclone.
In principle we could put that huge amount of energy into a suitable environment and then let the hurricane hit. (assuming we are also able to steer it, because, you know, you want to hit your enemy, not your headquarter).
But then, your goal is to hit rebels, not to generally destroy your land. Hurricanes or storms do not discriminate between friends or foes, they move rather slowly and announced, and if you get proper shelter you can survive them. You end up making more enemies (once non rebels know you did it, are they still going to support you?) and you make life easier for rebels by creating their perfect combat scenario for guerrilla warfare.
If you have the ability to manipulate that amount of energy it is more worth putting it into a bomb, which will be nuke size.