Execution and Banishment: The Key to a Small Prison Population

It in interesting to note that Geneva’s prison

Did not house any long-term prisoners. Imprisonment for long periods of time was simply not a punishment used in sixteenth-century Geneva. Even people sentenced to life in prison as the result of criminal trial were usually released within a few months, often paroled to the custody of relatives. Most prison sentences lasted only a few days (Witte and Kingdon, p. 69).

There were several reasons for this, but two of the major ones were:
Geneva executed for a lot more crimes than we do. Witte and Kingdon note that

Criminal punishments would involve…to a degree we would find appalling, capital punishment by a town executioner hired by the city for the purpose. There were a number of rather gruesome ways in which capital punishment was administered. Traitors might be beheaded, thieves hanged, notorious adulteresses drowned, heretics or witches burned. Every city of the period maintained an execution ground, usually with several rotting corpses of executed criminals on display, to let visitors know that this community maintained law and order. 

It is important to note that the Consistory, which I discussed in an earlier blog post, did not have the power of the sword. They could only recommend the civil court look into something and the civil court would decide the appropriate punishment. The Consistory could neither decide someone should be executed nor carry it out, although there was interaction between the civil courts and the pastors of Geneva. 
Also Geneva banished serious offenders from the city. Throughout the book Witte and Kingdon note that often those who would not receive instruction or committed serious sins or crimes were to get out of the city or be whipped and some cases executed. One example they cite is a man and wife who ran a brothel. They were given seven days to get out of Geneva. If they ever came back they would be whipped and then driven out again. 
The prison population was small and the terms short because serious crimes were dealt with by execution or banishment.