It's not necessary that the Kingdom of Aronia's capital was the same place as Rupanda so we can't actually assume that Aronia was established in the same place as Toran. Harmonia made Rupanda the capital not Aronia. It's very likely that Rupanda was established from another land that Harmonia conquered after they defeated the Kingdom of Aronia. But, that is something interesting to look into. But, I think Toran was established from Harmonia and not the other way around.
And as far as the government surviving, you don't have to demolish the whole governmental system when you split. Kranach could have left the governmental system in place, but altered some of it a bit. Rupanda was a thriving city before Kranach Rugner took over so it would have been in his best interest to leave some of the system functioning. Besides, it is incredibly difficult to build a ruling system over from scratch. It's better to do it from a pre-existing foundation. I'm sure Kranach changed a few things, though.