The French Embassy in Gaborone doesn't issue visas.
The French Consulate in Johannesburg, South Africa processes visas applications for people residing in Botswana.
To complete your online application you must select South Africa as your country of submission of application. You must then file your application with the French Consulate in Johannesburg after making an appointment by email at least ten days in advance.
Appointments are from Monday to Thursday between 9:00 a.m. and 10:30 a.m.