Do you mind if I drop a few spoilers in order to discuss some tactics?
Well spoilerth. Eff it.
Do not kill everyone on board. That is all.
Fire bombs are nice. I like breacher bombs myself. They're pretty essential for getting around that ship's insanely high dodge and shields. I virtually always settle in on nuking the missile command first, followed by the ion cannon. After that she's pretty well neutered.
Then it's on to the engines to remove the dodge and everything else generally follows.
