I've seen some suggestions people have made about commercial ships holding military space and a lot of people contesting it and whatnot, so I'll toss in some two-cents:
How about a ship module that is individually design-able, considered a "commercial" design, but is designed from Class-design and researched? Call it a Mission-module, and have it work like such;
-A mission module can consist of military weaponry, power plants, etc, though it cannot hold any engines, shields, armor, crew quarters, spinally mounted weaponry, or many large civilian components (cargo holds, orbital habitats, etc). It's components are considered "internal" to the parent ship.
-A portion of the module's tonnage (either static based on tech level, or a percentage) is "attachement tonnage", just overhead for this strange piece of hardware.
-A mission module has to be assigned it's own engineering spaces separate from the parent ship, as well as crew and the likes. It uses the parent ship's deployment time and shares maintenance supplies with such, but has it's own isolated maintenance clock and component failures, much like a naval ship. The failures do not affect the commercial components, though.
-A mission module can be independently targeted from it's parent ship, and sensor data will report it's tonnage within the ship, while still being detectable at the same active range bands of the overall ship. All damage is applied to the parent ship's armor, then either randomly or specifically to the module, depending on whether the whole ship or just the module was targeted. All internal explosions propagate randomly and indiscriminately between the two.
-A mission module has it's own independent "destroy condition" similar to how larger ships roll for destruction. When a mission module is destroyed, all of it's internal components are considered destroyed, though the commercial ship stays intact for this particular check. If damage is dealt to a destroyed mission module internal-component, it rerolls to another random component in the module or the entire ship, depending on targeting. If the whole module is destroyed when it's components are checked, the entire ship is rolled instead. The HTK "20 failed rolls" ship death check will still apply if the module is hit by a ship-encompassing roll.
Anyhow, that's all the ideas I have for now. Wouldn't say they're great, but at least interesting. What do you think, Steve?