I would do it the other way around. For repairs you need the trained military specialist crew; but reloading should be possible (on a second thought, does that not also need a specially trained crew?. Maybe it is best that both cannot be done on the civs).
The metagame reason is that this is intended to let us make proper repair ships, which will need to be civilian. If you let big ships reload their launchers in the field, it might well make box launchers too powerful.
But IRL, almost all warships these days are built at civilian-owned yards, and a lot of refits take place there, too. The USS Cole was repaired in Pascagoula, Mississippi, a civilian yard.