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He's obviously not afraid of that, cause he literally created a system that allows exactly that in the least kosher way possible. Literal genocide en masse w/o any risk, cost, prevention system or anything. All with bigger rewards than the normal state of the location.
As for how you design those wars. Do them inside out. Instead of their target being another guild, make the war related to the content. POIs will have quests and NPCs related to them. Make those NPCs know the respawn window of the biggest thing in the POI and/or have a quest related to the POI as a whole. The big target would require a higher wardec cost, while the general POI contest wardec could be cheaper, but with a more limited potential list of targets.
The guild that's present at the POI within the respawn window can declare war on several other guilds right on the spot, by using an item they get from npc/quest. Those items are limited in use by power differences between warring guilds, by POI's value, lvl of content, etc etc. They also have prerequisite costs related to them, either by doing something for the POI's node or by going through a guild-quest.
Using those items creates several "monuments", around the POI, that can be activated by the wardec targets. These monuments enable certain mechanics on the boss or around the POI in the vicinity of the wardeccing guild. This could range from environmental hazards to full boss buffs with adds and stuff.
If a single guild become a target of several such wardecs, they get the right to use secret passages through the POI (these could be tunnels, invisible paths on top of walls, etc).
If the game registers massive acitivity of players, with several warring guilds active in the POI - the entire place becomes a last mang standing arena, with all monuments activated and external entrances only being open one-way and single-use, so anyone who dies within the POI (being in one of the warring guilds) can resurrect outside and re-enter the location once (could be several times, but that's up to testing).
Once only one guild remains - the boss' spawn timer could be shortened or the spawn itself started, but with the place on lockdown, this boss would now be stronger (+the monument activations).
To me THIS sounds like a PvX encounter, where people on all sides agree to participate, where random people who're still inside the dungeon could still remain there, but would be in great danger because high player activity has "awakened the eeeeevil". And hell, you could even have extra rewards related to monument activation, so that everyone in the POI gets the appropriate lvls of risk/reward balancing.
And this is just a random idea that I came up with right on the spot. Obviously it's not ideal and it's nowhere near balanced. But it's also obviously way more complex than just "duhhh, pvp zone, duuuhhh", so it'd require a ton of coding, quest/event hooks, environment design/layout, mob AI and pathing, proper anti-zerg mechanics, proper boss design - all with, ideally, ONLY GEAR DECAY AS DEATH PENALTIES. People would have already paid to participate in the war and there'd be a lock out, so there's no damn reason to make players lose stuff!!
I bet there's like 10 other equally as in-depth and interesting (and more) ideas out there - all infinitely better than fucking lawless zones.