Crafty players might convert homing torpedoes to energy. You can also have a script command to destroy all torpedoes in storage, but a mission script cannot destroy torpedoes in the tubes.
"Damn the torpedoes! Four bells, Captain Drayton!"
(Likely actual words of Admiral David Farragut, USN, at the battle of Mobile Bay. Four bells was the signal for the engine room to make full steam ahead).