If you're at war with the rebels (or any faction for that matter) but would like to trade with them, the thing to do is break contact, if possible. To do this you first need to ensure that you're not besieging any of their castles, and that you don't share any borders with them, which is not always possible of course. After this you should move your ships away from their coasts for one full year. This should achieve a ceasefire, and get trade going again.