It's a bit annoying that the current combat system is all-or-nothing. I think that as in Civ V it should be possible for two relatively evenly matched sides in a battle not to kill each other off completely; it's very immersion-breaking that the system is all-or-nothing. Furthermore, it should be possible to capture undefended colony ships and constructors rather than destroy them.
I remember it was mentioned in the dev streams that such combat would not be implemented so that the player would have an easier time clearing up the pirates. To resolve this problem pirates could simply receive a penalty to repair rate.