It has been quite a while since I researched the topic, but I would suggest that Hermeticism, which encompassed alchemy and astrology, based on the writings of the apocryphal Hermes Trismegistus, might qualify. It flourished during and after the Renaissance and has many of the allegorical and mystical aspects that you describe.

It's degree of tolerance is something I believe varied over time. Giordano Bruno was executed for his heterodoxy, and his ideas emerge from the Hermetic tradition. Perhaps someone more knowledgeable can come along and elaborate.

Though I sadly do not have access to my copy (hence my vagueness on the topic) Giordano Bruno and the Hermetic Tradition by Francis Yeates is a fantastic introduction to the topic.