I have some questions about the relationship of the faerie with respect to the magical realm.
What is the difference between the faerie realm and the magical realm? Why does there not seem to be any pre-Quendalen faerie magic traditions in the order? Were all the classical magical traditions aligned with the magical realm? Where does the faerie realm come from?
Faerie is defined by its interaction with humans. Magic just is.
Happenstance?
Depending on your definition of "classical", no.
From stories and legends.
Some of these questions won't be answered until ROP:F is realeased. But the core rules and HoH:MC provides some detail, have you read them?
I don't know that cannon stipulates that there were no magical traditions wielding Faerie Magic before Quaendalon introduced it to the House (although my memory may be failing me). It is entirely possible that some esoteric lineage or hidden mystery cult practices Faerie Magic, and did so before Quaendalon's time. He was the one that introduced it as an exoteric Mystery in the early days of the Order - I don't see why that's a problem. Faerie Magic is a Mystery, and so had to be introduced into Hermetic magic by someone. It just so happened that it was adopted by a whole House that was also open about this "secret", making it famous and fairly accessible throughout the Order.
IIRC the ArM5 line preserves the Line of Muj lineage of Tremere, for example, which wield Faerie Magic. I suspect Ex Misc will have its share of Faerie Magic lineages as well, or other adaptations of faerie magic to the Hermetic system.
All the classical magical traditions were aligned with the magical realm by definition. I'd imagine classical supernatural traditions may have been aligned with all Realms. Taking just the Gnostics, there are I think now Magical (TMRE), Infernal (RoP:TI), and Divine (RoP:TD) exemplars in ArM5 supplements.
The typical classical magical cult would have been, I imagine, a Theurgic cult venerating daimon patrons of magic such as Hecate, Hermes, and Isis. These would have been magical cults, thier priests wielding power over spirits, and engaging in necromancy (speaking and calling to the dead) and divination (by various means).
The typical pagan worship would have been directed at non-magical deities, essentially worshiping powerful faeries. Their priests would have wielded powers more akin to Faerie Magic and related Mysteries: awakening, calling, and bargaining with faeries, and wielding powers as "gifts from the gods" related to their god's and their faerie allies' powers.
That's a matter for wild conjecture, certainly until the two missing RoP books are released. It suspect the question will not be answered authoritavely even then, and we will remain with "in-character" theories.
So far, it seems that the Magical realm is a realm of Platonic ideals and perfection, emanating from and being a pale reflection of the Divine (itself being a pale reflection of the perfection of God). The Faerie realm, in contrast, is a construct of human imagination, perhaps being the shadows cast by mortal minds when struck by the light of the magical or divine realm. (The Infernal is utter darkness, totaly removed from God's light.)
Other theories abound, but this seems to me to be the theory most consistently presented in ArM5 prodcuts and in accordance with the metaphysical structure laid down in the product line (and hidden from the PCs).
Also, regarding the matter of pagan religions and realms, David Chart had this to say in another thread: