How many story related missions do i have to finish until i am really free and can go where i want and do what i want to do? (number or good guess plz!)

I paid $5000 for the location coordinates of a jumphole to find out that i'm not allowed to use it that sucks. That was right before mission 5. After that mission every ship in Liberty fires at me, which makes it nearly impossible to use any trade routes there, so all gathered information about prices is worthless. So do i have to start all over in Bretonia system?

thanks for any help
Needa