A suggestion:
Pirates should have more of a tendency to attack sectors near a sector they own (one with a lone shipyard in it, for instance) or have even a speck of influence over. That way, certain sectors are pirate-free (though Xsotan still have a small chance to spawn) and that leaves free space relatively alone if it's not considered part of a "trade route" or other specified place that civilian spacecraft tend to go to when trying to travel inbetween two sectors. Said routes are probably going to be implemented in a much later patch, I imagine, but hey, this is a short-term solution.