This quest is indeed bugged. With the Proton Torpedoes equipped the shield generators are impenetrable with normal missiles and blasters. Unequip the PT's and they are destroyable just as normal, mission complete, but you cannot get the Bonus for destroying the tower. Tried it 3 times and each time I couldn't make a dent in them with PT's eqiupped. Needs to be looked at by the devs.