Was not the Collasus (under patch 1.1) disabled to stop a bug from v.0 where it attacking the priate base way north of there and the laset Tower firing caused a savegame curruption bug? It is in the read txt of the patch.
If you re-enable the Collosus to attack, will not cause the bug to re-appear? Or for that matter, anything that causes the Pirate bases Laser Towers to fire?
The lasertower issue was a big in the code where a lasertower that was off the grid by a certain distance would cause the game to crash when it fired. They fixed the bug, so now lasertowers off the edge of the map don't do this any more.
As mentioned in the instructions, though, if you don't want the ship to attack enemies past the edge of the map, then you can use the ForceProtectLocation scriptlet that will allow you to set a location and a radius for the ship to protect. The ship will then not engage any ship beyond that kill radius from the location you specify.
You were warned... pirates will be hunted down like vermin.