Hang on there. Now this is a mission which has given people a lot of trouble, but I have completed it many times, and I know it's possible. I think the problem you had may have something to do with your sister aborting her mission, which happens if they get too close or something. Whatever.
The best way to compelte this mission, in my experience, is as follows. Play the mission and check where the assault shuttle (I think it is) comes out of hyperspace. Restart the mission and wait near there. As soon as it appears, let loose with your torpedos (or rockets if you can take them on that mission). You can nail it before anything is deployed.