GotF briefly talks on page 27 about how "some gilds (the older ones particularly) might have unique ceremonies that relate to that gild only, but these have a symbolic rather than ritual purpose." Did anyone incorporate some into their game? Or have ideas to contribute?
I am sure that Iacob (p.107) has lots of ideas, if you use him in your saga.
I'm sure at least one of them has the aspirant spend a night as the gilds namesake via MuCo(He)? in some aura in the Forest's remnant parts. Whether or not its only symbolic, or what happens if someone tries it with the tree/aura of the defunct (Diedne?) gild, who knows?
I can see that more for the more nature-oriented Gild
Such as? Somehow I see the religion mostly directed at the mundane, and not necessarily something the Tribunal would be exposed to - with the risk of being charged for interference. Do you see it differently? How would you use him?
You can always take ideas from modern day masonic orders. The Free Masons and their "side degrees" such as the Shriners (Ancient Arabic Order of the Nobles of the Mystic Shrine), while typically secretive, often have some publicly known ceremonies. Many of their ceremonies have roots far older than the actual organizations.
You can also look to other groups such as the Knights of Columbus.
Commonly groups like this base their ceremonies on a recreation of some event that the group considers important. Applying the same thing to the Rhine Gilds, you can come up with events that fit the group ideology and design ceremonies that reenact those events. This would be especially true for ceremonies in which someone advanced in rank within the organization, reinforcing the groups ideology.
Jacob is (GotF p.107 box) easy to identify from the stories told by the religion's followers. Handri will cover him, but - as you say - Quaesitores may charge him for "interfering with mundanes".
The reasonable defense against this is a sufficient number of partisans at Tribunal - which should include all the Elder Gild.
Making young magi into partisans of the plans of Handri and Jacob is easiest done by involving them, and thereby implicating them, with spreading the new religion.
The Gild might e. g. have a rite of reconciliation with the faeries for all new members. This rite has the prophet Jacob present, and also some of his mundane followers expecting to be reconciled with the faeries - ah, angels - too.