To be precise, city formation is natural but the city environment itself is unnatural and causes disease.
Because the city environment differs from the regular environment, certainly cities have unique needs which country dwellers don't understand, and cities shouldn't be run from the countryside.
However, because living in a city drives you crazy, a fortiori the cities shouldn't be allowed to run the countryside. Cities should be considered socially underwater. They need to be quarantined so their madness doesn't affect anyone outside them. E.g. city-dwelling should be a hard disqualification for involvement in foreign policy, in exactly the same way you don't try to get an ideal trade agreement from someone dying of the flu.