I remember reading in the Forum about that.
As I didn't find that post I am opening this in order to give a solution or if maybe someone has a better idea to get it a step further.
I had that problem in small stores here in Greece. They didn't want to sell outside Europe, so the list of countries was massive and very difficult.
So the only way I found to do that Bulk and not going on echa countrie and deactivate was via Php MyAdmin.
I have a 1 line query that does it: UPDATE cscart_countries SET status = 'D' WHERE region != 'EU';
You can have that changed to whatever region you like to Deactivate.
You can also save that in a text file as countries_deactivate.sql for example then upload it to \var\database\backup and run it through the Administration → database → restore procedure.
Hope that helps someone.