The Prayer Warriors are actually mental parasites.Or rather fake personas created by the parasites for their hosts. Mary, the original host, found the perfect ideology for her purposes in madman Jerry and so the parasites are giving everyone personalities based on his. Most people are easily taken over by the fake personas, with demigods and wizards it's harder. Michael thought Mary ways the traitor and maybe Mary thought it too, but the parasites actually made her sleep with Percy Jackson to have more influence on him (he was already infected, otherwise Mary would probably not have been able to seduce him and he wouldn't have weird conversations with imaginary devils). When Jerry was losing his fight with Percy, the parsites joined their powers and Percy's fake persona finally took over. When a Prayer Warrior dies, the parsite simply jumps to a different host, using the same persona on this new host. The other parasites change perception and memory of their personas to make them not notice any difference. Whenever "god" is summoned to do anything, the parasites use powers they usually keep hidden to not attract too much attention (and cost lots of energy).
The reason Grover keeps coming back from the dead....Is because he is canonly accurate to Percy Jackson and the Olympians. He is simply turned to dust and returns.
The canon antagonists who cooperate with the Prayer Warriors do so in the hopes of achieving their original goalsVirtually all of the heroes who didn't join The Prayer Warriors end up dead, so it's possible that the villains like Draco and Luke are biding their time to wait for all of their enemies to die, then will betray the Prayer Warriors when the time is right. To quote BookObsesserNumberOne's sporking of Battle with the Witches, "Draco selling out Harry to a mass murderer. What a surprise."
Thomas and Ebony will be very disappointed in the next Republican administrationThe Prayer Warriors assume that people like John McCain, Joe Reardon and Mitt Romney support their cause, but given that said cause involves murdering everyone who disagrees with them and most Republicans don't go that far, it's possible that the next Republican president will do something they disapprove of, and they will then conclude that neither the Democrats nor the Republicans will give them what they want.
Ebony had divine intervention on her side when she killed Harry PotterConsider that while the Prayer Warriors have a large amount of Plot Armor and the favor of the author, they've never been able to defeat the main characters of the series without help.
Some one is going to write a troll fic to this storyThe fic will go to far in one of its jab. Bounes if it is a setting that is very broken like say Digimon or Nanoha, uses a dark power like say Beelzemon, and the writer is a christan (I am kind of tempted to do one).