In the chaos of the exodus, a great deal of theological confusion was introduced into the worship of existing deities. Even the Nine Immortals had their particular qualities muddled by the questionable grade of cleric that managed to make it through the flight to the Sunset Isles. Combined with the current apathy towards the seeming-unhelpful gods, many worshippers have a hard time explaining just exactly what the theological principles of their god are in the first place.
As such, clerics, favored souls, and other classes that choose Domains are allowed to pick Domains freely without conforming to a specific list for each deity. Contradictory domains such as Evil and Good will not be accepted, and any domain pairing that isn't fairly obviously compatible should be explained in the cleric's background. Clergy should make clear how they approach their god's general purpose and portfolio through the Domains they've chosen.
For the War domain, the favored weapon ability of Favored Souls, and the Spiritual Weapon spell, clerics can choose any one Simple or Martial weapon.