How would a deity best reform his Church?
The Beginning
A deity of good aspects (Justice, Light, etc.) has guided mankind since the dawn of Creation, helping them develop and prosper. He was always a powerhouse in terms of raw divine power, allowing him to directly intervene in the material plane through an avatar, up to and including his actual divine form. There were gods of other good aspects, (love, fertility, nature, etc.) the worship of which he also built up from nothing. By guiding mortals to them, their worship directly increased the good aspect's power. Unfortunately for our deity, however, he comes to find out that he was too far back in humanity's development. A negative aspect trickster deity who kept himself hidden, reveals his presence by sealing off the material plane, which prevents deities from directly interacting with it. After giving the trickster the god equivalent of a beating within an inch of his immortal life, our deity discovers to his horror that the damage has already been done, and the seal will remain in place for over a thousand years. Because humans were not developed enough, paper and writing isn't really a thing yet, and most of his teachings exist only oral tradition.
The Sealing
In terms of raw power, the gods were unaffected. They are as powerful before as they are after. 752
However, the Seal made direct intervention impossible, as well as making lesser actions more taxing. The other good aspects can eke out a weak blessing at best for some of their followers, while the main deity can still hand out lots of blessings of decent potency. Without the ability to speak to his followers, natural divergence is inevitable. Because of this, the Justice deity watches his Church slowly splinter off into sub factions before his very eyes. He allows this because it's splintered yet growing follower base continues to increase his power, increasing his indirect influence and because he can't stop it. As more time passes, however, the sub factions continue to splinter further, growing more extreme and eventually, begin to consume each other in wars and violence. One of the worst side effects is idolatry in that it subtracts from prayers to him. So a prayer to Justice + x is weaker than if it was just to him. The negative aspects also gradually begin to gain traction.
The Seal Ends
At this point, the seal finally ends, and the deity is able to intervene how he sees fit.
But how should he?
Obviously, nothing stops him from descending upon the Earth, and smiting those who act in his name to rape and slaughter others, and collapse the heretics' cathedrals one by one with a snap of his fingers.
But is that the best way?
He wants to put humanity back on the True Path, but without tearing the world asunder doing so. He also does not fear the negative aspects as they are, but fears what they are becoming.
The largest church (~40-50% of the followers) is the "most right", but even so, is so hilariously wrong and perverted from the original teachings that starting over completely may actually be easier than correcting it.
So, his ultimate goal is to completely reform the Church by removing all sub factions and checking the rising power of the negative aspects.
How should he do this to minimize suffering while still not compromising on his goal?
How would the fantasy medieval society react to him, and how should he react in turn?
Clarification
The established Churches have a vested interest in maintaining their power and position, so it would not be beyond possibility for them to gather up a thousand years worth of magical artifacts, and swing public belief to directly oppose the deity.
Inversely, if the deity acts too decisively and causes a lot of chaos by essentially alpha striking the church before they can respond, he may end up doing the opposite of what he wants by strengthening the negative aspects to a dangerous level. 752