The reason you are experiencing that problem is that in the very next mission you destroy that ship, it is scripted that way so that they ship cannot be destroyed. I ran into the same problem blasting Admiral Arai's ship in one of the Fed Missions. Just let the ship go, and if for some reason (like you were beating on him too much) he cant leave the sector on his own power, just tractor him off the map, but be careful not to get yourself pulled off the map with him.