I don't believe the minors have that much to do with the GD really. Yes, Waite was a member of the GD, but he identified himself as a Catholic Mystic and the bulk of his writings deal with mysticism. From his New Encyclopedia of Freemasonry:
"I am certain, as a Catholic Mystic, that in the first place we came forth out of the Great Mystery and that in the last we return...".......
There is nothing specifically Catholic about that statement, and Waite was never a member of the Roman Catholic Church as far as I know. Anyhow, Catholics (in the ordinary sense of the term) are certainly uncomfortable about Freemasonry, and Waite was not. If you are really interested in Waite's 'Catholicism' read
The Unknown Philosopher and
The Hidden Church of the Holy Grail. Waite's Christianity was about as orthodox as that of Thomas Jefferson and seems to be almost identical to that of Louis Claude de Saint-Martin. As there is no indication that Waite had any interest in the soteriological Christology of the Catholic Church, it is seriously doubtful that he even merited a place in Purgatory, much less Heaven.
ETA.
A New Light of Mysticism: Azoth; Or, The Star in the East is an early work by Waite which is quite candid about his 'Catholicism'. It does mention the passion of Christ as an allegory of our rejection of what he stands for, but no mention of the saving grace provided by the passion, which is the central, essential doctrine of all the main versions of Christianity, including Roman Catholicism.
Somewhere, maybe in the
Azoth book, Waite describes himself as 'an Uniate Catholic', which is too indefinite to mean much. At other times he uses the word 'Catholic' to mean 'universal', and he speaks of such things as the Catholic doctrine of Theosophy or the Catholic doctrine of Alchemy.
Sometimes I think I may be a Catholic, and maybe you are too, Abrac. Ravenest is a priest in the Ecclesia Gnostica Catholica.