They're not taking anything away from you for choosing a different nation, they're just giving you more for playing with people from the same nation. It's like having extra vendors or items for sale in ffxi for getting together with some people from the same nation and taking over a region.
The problem isn't in their method, the problem lies in the order in which the method was carried out. The pride should have been enlisted at start before the linkshells were formed. As you would have been more likely to be playing with people from your own nation already.