Hello,
It's actually pretty easy to delete area code for specific area. Simply go to Menu->Administrator->CommonData, select "View" on Calling_Codes array and search for 939. You will find Puerto Rico's code and you can simply delete the value. After that, no code will be added to contacts from Puerto Rico.
We'll take this information into the account on the next release and by default there won't be any code set for Puerto Rico for new installations, thank you for bringing this to our attention.
Kind regards,
Arek