This’d be a VFX solution, but what if Starkiller just obliterated most of what looked like almost the entire Republic fleet, rather than anything to do with a planet? That way you preserve all the political infrastructure, but leave the Resistance as the only real military throughout the films, before the Republic military recovers in time for the sequels.

This would also explain why it’s a civilian fleet that’s needed at the climax of TROS.

As I think we all know, JJ originally wanted to destroy Coruscant, but was told not to, presumably for exactly this reason, so that everything that preceded his movie wasn’t just casually undone.