Isn't it nice to turn things around when it benefits you?
You said it yourself. You were told to stop, multiple times, was CDed and intercepted. You had your chances for roleplay, which you ignored, insiting on running to your destination under pretense a lawful player might care for but can't take as credible for you to ship a good amount of contraband around the House it represents.
By the time you got shot down, you had multiple violations on you and complete refusal to cooperate with the Navy officer. Getting rid of violators and their cargo through the way of force is completely in the rights of any lawful player when dealing with a crafty and uncooperative violator. You've exhausted your chances when you initially didn't comply, and got consequences that have been coming to you.
P.S. Shooting at the ship and shouting for it to stop firing isn't how you express your wish to surrender the contraband.