Mimi, please, with all my respect:
I suggest you look for another accountant.
Seems that your employers might be evading taxs and, no matter what do you think or what do they tell you, you might be working under the table.
1. AFIP has all the info of the employeds that work legally, here you have been ill-advised when you assert that
"The problem is that we were not registered with AFIP which is also NOT required for a salaried employee".
Go to the AFIP website, use your cuil and password and take a look at "mis aportes", there you can double check if they are paying what they have to pay.
2. Employeds must pay ganancias if your salary is over 5782 pesos for single or married with less than 2 children. Marriage with 2 or more children pays only over 7998. You mentioned that you saved money, then you are over that minimum for sure.
http://www.afip.gov.ar/gananciasybienes/#empleados
I cntrl copy what the afip website says:
"Empleados en Relación de Dependencia
¿Quiénes están obligados a presentar declaraciones juradas anuales del Impuesto a las Ganancias y/o del Impuesto sobre los Bienes Personales?
Los empleados"
Asumming that you paid all the taxes as you assert and my speculations are wrong, as soon as the AFIP rejects you, you can start an amparo at Court. With corralito there were thousands of amparos and they won them all. They were slow because there were too many but right now there seems to be only one case.
Regards