I think the main thing to do to keep great story telling and end game multiplayer, you can release patches to put on new content (added stories/continued storyline). However, if they were to do something like the WAR Update in TF2, where the most demos/soldiers killed got a 4th item.
The developers simply have to create a new PvP environment. Depending on how different factions win, can affect the world for the next patch. For example, using WoW:
Alliance vs. Horde in some battlefield for territory, or whatever. After 2 months of PvP, a new patch would be released. If Horde won the most matches, they could have a new town of shops there, with new quests. Alliance would then retreat to another area, and get new quests to do with the loss - sabotage missions on the Horde captured area, for example - and possibly get control of the area again.
Adding things like that would increase competitiveness, give a reason to keep playing - for new content based on the player's actions, as well as constant new stories and quests that actually involve the player.
tl;dr Make new arenas. If Team X win, they get new stuff. If Team X lose, they still get stuff, but have a spin on their storyline.