Wouldn't they just have to add skills like "Starship Piloting" and "Starship Gunnery" to your character template?
As for upgrades to the Ebon Hawk, they could just be parts that give bonuses to supplement the PC's (or whomever is the pilot) specific skills. For instance, upgrading from a single laser cannon to a quad laser (like the Falcon has) would give, I dunno, a +1 to the gunner's gunnery skill, and add however extra damage above that of the original laser cannon.
But I think the main problem would be how the combat is actually handled. The turn-based/real time hybrid that they use for single combat might look rather silly in a space battle if you pause, click, pause, click for each action. But if they can find a way to do it I think that'd be a great new feature. It would actually make the Ebon Hawk valuable, and would make spending on upgrades an important part of the game.