I found that there's a sweet spot directly under the generators where u can position yourself, and shoot the hell out of them without getting shot at, then fly out clear and finish em off with a couple of shots.

A bit of a cop-out i know... ...but i took out one properly and knew i wouldn't survive unless i took some drastic action - LOVE the game! - Shame itz a little short

try starting the mission over. If I remember correctly, at the beginning of the mission, you can just use your cruise engines and cruise around until it updates your waypoint. I don't think you had to fight, just stay alive. This will help save your batteries. Equip a ton of torpedoes, they are cheap. And like the previous post said, try hitting the bottom, rocky portion of the generator.