Thank you very much Kano.
I did study that part of the readme word by word but the command didn't work as written, on my end. After many hours of trials, I found out what the issue was. I'm writing it extensively so anyone that comes across my same issue may benefit.
Sending the command cgminer-api disablepool|1 (as I understood from the readme) could not work because the symbol "|" has its own meaning in Linux and gets interpreted as such, and not as an option of cgminer-api command.
The correct syntax is therefore: cgminer-api "disablepool|1". This way it works with most pools.
In my case I can only disable some of the pools in the list, I need to study better how is that possible. My guess is that the pools i'm trying to remove are somehow hard-coded in cgminer configuration by some file where my account that has no write authority.