Primary weapon fire points are not subsystems, and cannot be destroyed without destroying the entire ship. They are not dependant on any subsystems being active, and function fully even with ships that have no subsystems at all. What you are experiencing is not a bug in WOD, as much as a 'feature' in freespace code.
If your ship has a weapons subsystem and turrets and that weapons subsystem happens to be destroyed, the turrets will get a downgrade in their ai e.g. fire more slowly and less accurately, but they will never go inactive unless you destroy the turrets themselves.