Instead of just going boom and damaging the user, I think that destroying destroyer modules should rend a unique effect for each module.
Engine: Causes damage as the user tries to use their forward engines. It should be heavy damage.
Capacitor: Should not be destroyed completely, but instead “leak” radiation that deals a large amount of damage to the destroyer and all ships within a certain radius of it. This should stay in effect until the module is repaired or en engineer restores the destroyer completely.
Pyro emitter: Because it is just a big gas gun, or flamethrower type weapon, it should explode violently, dealing extreme (nuke worthy) thermal damage in a wide area.
Plasma turret: Should break and begin spraying plasma out of it like a fountain, only damaging the shields of the destroyer as well as any other ship that passes through its small radius.
Blaster turret: Should just cause a minor explosion.
Multiphase shield: Should invert the shield so that it instead lets enemy fire in, and traps the user’s fire in.
Photon torpedo: Should cause several beams of light to randomly slice through the destroyer over a second or two, causing significant EM damage to it, as well as any enemy lucky enough to be hit by a beam.
Gravity lens: Should create an anomaly cratered on the destroyer that pulls ships in, but only damages the destroyer.
Hybrid missile: Drone missiles should spill out of the module without activating, but on impact deal high explosion damage.
Repulsor: Should just cause a minor explosion.
Wormhole generator: Should randomly teleport the user a random distance every few seconds until it regenerates. Each teleportation should deal light EM damage.
Destabilising field: Should create a field around the destroyer where this effect is temporary. Affects the destroyer and any ships in the small radius.
Tempest launcher: The unused missiles should all be dumped in to space and explode like mines on impact.
Isotope harvester: Should create a siphoning field around the destroyer where it’s shields are transferred to nearby ships. Allied or otherwise.
Remote minelayer: The unused mines should be dumped in to space and detonate after 3-8 seconds.