They kill the Navy and their mates as they whant to overthrow the goverment.
If you whant to be a terrorist you will most likely be oposing some govermet, even thouh the Council whants to do this they arent realy terrorists as they are oposing the navy openly, i would concider them one side in an civil war.
The mayor difference about terrorists is the fact that they fight for a higher idea instead of pirates who just whant cash.
So you should ask yourself if you whant to become some pirate who works for himself or a terrorist who works for some idea.