It is confusing language, because usually armies are deployed by the government in power, and wouldn't be helping a rebellion. I think there's a possibility of a transcription error. But looking at the words as you've given them, I think they were helping the rebels. If you put something loosely in the back of a truck, it is in the truck, but it could fall out. It is not safe. You "secure" it by tying it down. In the context of a military operation, the rebellion had happened, the rebels had won, but their victory wasn't secure. It might be temporary. They weren't in a strong position. There was a chance that the people they were fighting might take back what they had won. I believe that "secure the rebellion" means to reinforce the position, make it safer, make it permanent.

"Secure the rebellion" sounds to me more like he was supporting it than opposing it, but the language is unclear. Your choice of "suppress" would be much clearer if he's acting in opposition, and obviously "support" would be much clearer if he's acting to support it.