I generally consider "guilds" as we have them in game to be more like knightly orders or societies rather than as a craftsman's guild. Some of these could be quite prestigious.
As for why you might not want your titles used in non-religious letters, the perfect example is the Blood Cult on BT. The religion was widely hated, and I would imagine that the people involved did not want to go around advertising their affiliation. This change would force a certain percentage of nobles to advertise their faith whether they want to or not. (And yes, I know that it is public for lords. This is circumventable by not becoming a lord, and it is also a local phenomenon, not broadcast constantly with every letter you send.)
