What new story elements could arise? “The [opposing faction] found a new [thing] that stands to [undesirable outcome] everything that [our faction] [loves/hates]. We have to [action] the [thing] before the [opposing faction] [does/can use it/destroys it].”
That’s the entirety of the faction conflict in that sentence right there. Done and dusted.
It is the World of Warcraft. The events of WarCraft happen in that world, but there should be possibilities outside of the factions and the factions shouldn’t even necessarily be the center stage players.
Again, it would have been far healthier for the game to not only not be forced into a faction based on character creation but also to have both factions, the Horde and Alliance, be these unknowable, almost eldritch entities with how massive and distant they are from the common adventurer that pluck away lives to serve in some unstoppable war machine that grinds people to dust no matter their race. We adventure around them, not for them.
Resentment can absolutely boil, but that’s why they would be rogue elements. The official Alliance/Horde stance is that hostilities have ceased, end of discussion. If you want to buck that and go settle old scores, you do so without the support or approval of your faction.