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But, as Noaani said, that is the case currently. The strongest few guilds will control the majority of pve content (especially bosses), because they'll be able to push anyone else out of the encounter through pvp. At which point all the other guilds simply don't have the access to pve content.
I definitely hope that the world is huge and populated enough to provide everyone with enough mid-high quality pve, with the top quality stuff being limited to power checks.
I think the easiest way to do this is with party/raid quests and "cage" triggers. Maybe there's an npc you gotta bring to a location, at which point he triggers a fight in a "cage" and then you gotta bring that npc back, but he's now a target for other people and if they kill him - your reward's gone. Or you get a key for a room in an open dungeon, where the fight happens, and you then need to go deeper into the dungeon to get your loot, but your group is now perma-flagged until you get the loot or wipe.
In other words, you have assured pve content, but you still have high risk of losing the reward for it due to pvp.