Last time an MMO introduced a 3rd faction they started to die out faster then any other MMO created (CoH/V).
2 Faction MMOs work fine, its how they are managed by the devs and the players. WoW is the most successful with 2 major factions and they have the biggest balance issues when it comes to their PvP server populations, ToR will be fine, as well it is STILL far to early to make any real judgment so the foilhats are not needed.
WoW PvP only works because the great majority of it is instanced and the cross server system helps to cut down on the queue times generated by the faction imbalances. The only part that wasn't instanced when I last played (Wintergrasp) was a total flop - at least on my server.