We need a distinction between 'systems to avoid' -- meaning ALL ships stay out, and 'systems for unarmed ships to avoid' meaning hostilities are in progress.
So, 'combat zone' systems? A two-tiered system of flags isn't very complicated. MM might be able to add it to the next beta.
With combat zone systems flagged, when the colonizer plots its course it could just re-route until it found a safe way to its destination. Meanwhile, warships would be able to go ahead and take a direct route to where-ever they were going, except for 'systems to avoid' which would still be totally off-limits.