Part of the reason I post demographic and economic information is it gives a sense of the resources various temples, rulers, and other groups might have. Hopefully it is clear that the Lunar Empire is by no means all-powerful. It has money (or at least it did until the wars in Dragon Pass drained all of that), soldiers, and a powerful College of Magic. But those resources are finite.
The most determined foe of the Lunar Empire for the last century or so since the Nights of Horrors has been the Orlanth cult. It also traditionally controls the strategic area of Dragon Pass and its lucrative trade routes. The Red Emperor has expended vast treasures trying to secure Dragon Pass and its trade riches for the Lunar Empire. To do that has meant taking actions to weaken that cult.
In New Pavis – a major Lunar garrison – the Lunar governor kept the temple to Orlanth opened until 1621. Boldhome’s great temples were closed. But worship of Orlanth continued in smaller groups even then (the Boldhome Pockets were notorious for their near-open Orlanth worship).
Now that’s easy to do in your garrison cities where the bulk of the Lunar Army is. But what do you do elsewhere? And what do you do in the Provinces?
The Lunar Empire tends to follow a simple strategy outside of the garrison cities – disincentive the Orlanth cult through patronage, install friendly clients were possible, and resettle rebellious populaces if necessary. But don’t worry too much or spend too much of your limited resources on this – let the local client rulers do your work for you. Most importantly, make sure no new Jannisor appears, who is capable of leading confederations of foes. I mean after all, the Orlanth cult is hardly as dangerous as the Pentan nomads – eventually even Dara Happa became a loyal and intrinsic part of the Lunar Empire.
The ambitious tend to look to the Empire to support their ambitions. As long as you make your demands easy, the ambitious will come to you. Heck, many of the rebels can easily come to accommodation with you.
You just want to hope your enemies are all Parmenion, and not Alexander.
The other thing the Lunars tend to do upon conquering a barbarian land is killing the old ruling house. You don’t hear anything Pyjeemsab’s other family members and their descendants. And Lunar assassins did a pretty good job of trimming the descendants of Sartar.