For better compatability with other mods, I suggest you copy the

/xyz/data/equipment/weapon_equip.ini

into the corresponding freelancer folder and then delete the
equipment folder from the mod.  Of course, if it were me, I'd
make a backup of the original game file first.

This modification allows you to mount missiles onto the torpedo
hardpoints and it changes nothing else. It should not cause any
conflicts if used as I suggest here.