Geneva never was a theocracy (total submission of the State to the Church) and Calvin never favoured that. He rather had to fight against the reverse, the control of the State over the Church.
Back in Geneva in 1541, Calvin drafted the text to be later discussed with the city's councils, in which he clearly defined the power of the Church and the power of the City. The purpose was not an early separation of the Church from the State, but the sharing of the tasks.
The question of excommunication was central to the debate between the magistrate (civil authority) and the company of pastors. Was the excommunication (interdiction to take part in the Eucharist) a religious or a civil decision ?
Calvin defended the first interpretation. The city councils wanted to keep the privilege of excommunicating. The company of pastors had to wage a long and difficult battle before winning the case.
The civil authority also intervened in the nomination of pastors, once they had been co-opted by their peers, in the rebuking of undeserving pastors, following the guild's advice.
The power of the Consistory is restricted by the magistrate's appeal ability in many cases.