The events of the Godtime eternally recur within Time. Each dusk, Orlanth slays Yelm and sends him off to the Underworld. Each dawn, Yelm rises triumphant from Hell, heralded by Theya. The cosmos is in a constant kaleidoscope of destruction and creation, of harmony and disorder, of movement and statis, etc., while the elements go through their cycles. The gods do not have free will about this – it is a condition of their immortality and the Cosmic Compromise.
This is accepted by most Gloranthan religions – certainly by the Orlanthi and the God Learners, and those they have influenced (such as Peloria, Prax, etc.). This applies even to the Red Goddess, who made herself part of the cosmic order through the Battle of Castle Blue and her rise to the Middle Air as the Red Moon.
However, the mortal worshipers of the gods do have free will, and so the gods can act through their cults. Orlanth can act through his cult, as can the Red Goddess. The Red Emperor, a demigod, maintains his free will and his divine power. Other such powerful individuals act within Time – Harrek the Berserk, Androgeus, Jar-eel, Argrath, Ethilrist, etc.
This helps explain history – kingdoms rise and fall, aided by their gods and opposed by other gods. Hostile cults may cooperate and friendly cults may be rivals. That is in the nature of mortals. For example, the gods of the High Council of the Lands of Genertela included such rivals as Orlanth, Zorak Zoran, Aldrya, and even Mostal. The Lord Demon of the Legions of Death led armies of trolls to fight alongside Humakt and Orlanth.
The Lunar Empire is arguably different, as it is the first Genertelan Empire that openly embraces the one power all of the gods fear and hate – Chaos. And yet the Lunar Empire also associates with many of the gods that uphold the cosmos especially the celestial gods of Fire and Sky. It is a contradiction, and one that confounds many of their foes. Even their magic is different, with the power of the Red Goddess constantly waxing and waning in accordance with her cycles (except within the Glowline).
As a result, the Red Goddess is locked in conflict with many of those deities who must fight Chaos as part of their existence. But her cult and their allies are made up of mortals who must make their own decisions. They are guided by the Red Emperor, but the Red Emperor is not the Red Goddess (merely her viceroy within Time).
Now for most of our characters, we are likely content to simply surf along these issues. But some campaigns might dive deep into this and explore the possibilities. But as mortals, it is your choice!