You can keep the Church of the Chosen Ones,just do not ignore the event of two survivors overthrowing the Church,otherwise all of your survivors will suicide. The reason for keeping the Church at first,is to gain happiness bonuses that may be critical. Just overthrow it later and everything will return to normal. Also do not ban the book before the church,for there are no negative consequences if you do.
I just want to point out that,once you get Kruggy,Jackon and Jayson,keep them for the rest of the game,for fourth slot use either Kim or Reinald.
The buffs that Kruggy and Jayson provide are invaluable in the late game,while Jackon has such an amazing dance,that it freezes time for ~5 seconds,which lets you do precise clicks with Virus and spawn other special zombies.