I wasn´t actually worried about having the same spell on two domains, since it creates the same kind of problem the player faces when he doesn´t own the splatbook. I assumed -same as you posted- that since the two domais have equal validity, both spell levels should be correct, and therefore legal. My concern, which seen in perspective is very little, was that a unique spell in the ranger, paladin or adept list could go in a new domain, invalidating the old level; this is what was called "level dance",
not the possibility of more than one level
on different domains. The number of candidate spells is very low, but as a theoretical construt, it´s possible, and (among others?) include the following spells (I don´t have the 3.5 DMG handy, but I suppose the Adept list hasn´t changed a lot since 3.0): Sleep,
Burning hands, Mirror Image, See invisibility, Web, Lightning Bolt, Wall of Fire,
Minor Creation and possibly one polymorph spell.
Notice that after making the list I had to remove two spells that were already in some domain with the correct level. It´s a major hassle to double check every domain to make sure you got it right; or course it only happens with non-cleric, non-druid spells, but those are exactly the kind of spells the archivist´player is looking for

.
On a unrelated tangent, notice how banning paladin and ranger only spells* is the equivalent of banning their entire spell list, since the non-banned come from the higher priority Cleric or Druid list anyway and for all effects, don´count: it´s like if they didn´t exists. Careful, I don´t see it as a bad thing because most of those unique are unusable by the archivist anyway, since they deal with mounts, animal companions or favored enemies, or their level are calculated for when the paladin or ranger can get them and not having the Archivist in mind.
*I mean those that
only appear on paladin or ranger spell lists.
So, I don´t see as a too bad solution to ban Paladin and Ranger lists and move Domains behind Adepts.