Even though it would be unbalanced, it'd be fun for a while to see, say, the top 100 guilds flock to one side and deny the new favour system for about a week or so.
But I have faith in Anet's ability to make the game fair.
anyway, Qual is right in the sense gameplay seems cooler if your on the weaker side. They might approach it like Alliance and Horde in WoW, though I don't know how Blizzard manged to keep it equalized.
You should not forget that WoW has more then 1 server, while GW has actually one server. (at least to us it seems that way)
WoW has some servers which are not balanced in which the Horde is smaller then alliance.
I think Anet can do this really well, maybe they even have some bonuses they will implement on the weaker side so that then again people will choose for the weaker side and things will balance out.