If I'm assuming your in the correct mission, there's a simple way of doing this. Refit your ship so it has high manouverability, and high shields. Next go into the mission, tractor the pirate near to the sun, and the debris will start tearing apart his shields. Fire at will, then let him go, warp back to the freightor, then simply start firing at it. Finally, when its shields go down (if it takes to long do as before but only enough to let its shields go down, not destroy it), then start transporting people to take over the ship.
You should now have the freighter captured, and the pirate destroyed.