I know this is a hard decision to make because you earn lots of cash selling alliance change tokens. But this is better for the game.
Because right now you are fine if you look for cyro/IC guilds of your alliance. The problem arises when you have casual guild which does everything, including progression trials and PvP.
When you try to lead PvP in such a guild, lots of guildmates will have PvP character.. but in other faction. And I'd say roughly 50% players don't join because of that.s
Think of it. Players have what it has to PvP, they are willing to PvP, but don't run the content just because of this system.
So, what should be done: every character have no faction until they sign up for a faction at any campaign. Faction erases at the end of campaign.
And you can even leave faction change tokens in the store, for those who want to switch mid campaign.