Um unless the marines board via teleportation could you not salvage the ships they board with?
Yes, you already salvage the ships. The question was how do you salvage the corpses of the enemy marines?
easy. You salvage their equipment. This IS a space game, they're not walking around in earth like uniforms, they're wearing high-tech equipment/blasters, ect. So when you board the ships, you salvage what you can of their equipment too.
I say, salvage the bodies and use them in the Biofarms (as in dead marines becomes a Biofarm item). Or that something like "X of the enemys marines gave up and joined your fleet.".