That's such a bummer if so. It sucks wanting to play as one race but all your friends are on the other faction. It also doesn't work as well when you have a lower population game. And let's face it, that's what this game is going to be. It's not going to get WoW numbers, so designing a game expecting that is foolish.
You could also make several characters from different factions. Whether for PvP, PvE or to know their point of view of the races, why they are or from the same factions, history, etc.