Sadly the story-required pirates are hard to avoid.
For instance. The mission after you jump to Elio. Even using 2nd grade fighters and weapons, I still blow up the second I try to defend the freighters. It's as if every enemy within miles goes, "I MUST SHOOT THIS GUY." And somehow, despite having obtained hammerheads armed with tetsubos and full compliments of missiles, I STILL get maybe one, two kills.