Border skirmishes, adventurers settling old grudges, occasional fights over resources--things the leadership has shown before they're willing to overlook as the cost of sharing the planet, as back in the pre-WotLK days. Rated PvP could actually be migrated into the lore as high-risk live-fire exercises (where they're not intentionally trying to get people killed but accidents and "accidents" happen: the same justification for lethal PvP in FFXIV despite the three main nations all being close-knit allies), especially since PvP right now has just as much a chance of fighting your own faction as the other in rated/matchmade play.
War Mode requires no changes in a relaxed PvE barrier, see above re: adventurers settling grudges.