The Self Destruct codes might be the easiest most efficient way to blow up a Star Ship, but, there is more than one way to skin a cat.
Setting the transporter to beam HALF the warp core into the torpedo cache comes to mind.
Turning off the navigation shields.
Supercharging the gravity overloading the structural integrity field.
Replacing the atmosphere with something flammable.
Creating Holographic super powered super soldiers to... hells even a holographic bomb would exact a real explosion if the safeties are off.
But the letter of the law is simple, the Hirogen under no circumstance should be allowed to walk away with advanced Federation technology that they can use to alter the galactic balance of power.