This trick is really simple to do - before casting armageddon, reach an enemy reincarnation site and sink it completly 

(the pillars will not sink, only the terrain). After this is done, cast armageddon - now the tribe which you sink

the reincarnation site will not get hosted to the armageddon site, because they will die before it happens.

Why does this happen? Well, during the initialization of Armageddon, the game teleports all of the tribes' followers to their respective start locations (the center of their Shaman's Reincarnation Site). Once the arena is formed, the game will teleport all of the followers to the arena, one by one.

 

In order to kill off the tribe, it is your task to send these followers "to the depths" during the Armageddon Initialization process. To do so, you must submerge the entire tribe's Reincarnation Site(Pillars and all) into the water. Make sure you can do this and cast Armageddon before the enemy shaman either rises the Reincarnation Site or Reincarnates, else your efforts will be wasted.

 

As mentioned before, the effect results in the complete elimination of the tribe who is on the receiving end of this trick. When the arena begins to form, that tribe will die off and they will be out of the game. It should be noted, in some instances, Populous will exhibit some unusual behavior after performing this trick.