1) It's in Book of Exalted Deeds, Apostle of Peace 9, Herald 9, Exalted Arcanist 9. Transmutation [Good]. It appears on different spell lists than the cleric version and Spell Compendium doesn't say that they're the same spell.
2) The Sanctified spell (Greater Luminous Armor) is cast using Miracle, and the Archivist (And other casters for that matter) don't have restrictions on what alignment spells they can cast. I do agree that it's rather Wrong, but hey, Rai doesn't think he's actually evil.
On the Wish and the Word: Not only are they relying on an item for initial startup, it's an illegal item, and every thing the Wish does can be stamped on by a DM. Additionally, the FaQ specifically calls out Innate Spell as not qualifying for Supernatural Transformation... I still love the duo.
As for the match between this Team and the Wish and the Word, we're immune to the blasphemy/holy word/word of chaos/word of balance line, and cleaning up the wish is as simple as gating them into a Selective Spell'd (The spellguard ability, excluding Dragon type) AMF while Saphiron beats the stuffing out of them. No contigent wishes, no wishes full stop and a big dragon who can freely beat you up.
EDIT: Updating the OP with more information.