In order to reflect this I've stripped the alignments from the deities in my campaign and given them rough spheres of power. Usually, each gawd will have two: one that represents the good things about the gawd, and one that represents its wrath, allowing the gawd to use a carrot-and-stick method with its followers and heretics.
For example: the healing badger, Mortitagus, primarily the gawd of healing and nature. His spheres include anything to do with those two things, including plagues, which he sends when he feels his Houses of Healing are not being frequented enough. This has lead to a more radical faction within his faith that jumps people in the streets, beats them to an inch of their life, and then takes them to get healed by their priest. Their thought is that beating up a few people in the street is worth not having a terrible plague ripe through the land so therefore it's an act of mercy.
This conflicts somewhat with the Hackmaster system, which uses the Kingdoms of Kalamar pantheon on its basis for clerics. There is an easy fix to this.
Each different cleric represents a way to worship your gawd of choice. The best way to show this is an example I feel.
The Andalish gawdess the Morrigan has three major spheres: Sovereignty, Death, and Honorable Warfare.
A player wanting to focus on the Morrigan's power over Sovereigns may choose the Courts of Justice, changing (with the permission of myself) his ornate god armor in constantly buying new crow-feather cloaks or ceremonial swords.
Additionally, a different player may also want to focus on sovereignty, but not having a cleric of noble birth, he decides that instead, he'll focus on being a councilor to a ruler. He needs to be as wise as possible and to have a variety of skills that will benefit his king, so he picks the Order of Thought.
Both players worship the same gawdess and are part of the same faith, both even revere the same power, but both approach their faith differently. One is LG and the other is LN.
While some churches may make more sense and are easier to fit to a particular gawd and gawdess but it's only limited by your imagination on the matter and what you can make sense of theologically.
You can also, with permission make minor changes to the church to make it fit better fluff-wise. Like having a cleric of Mortitagus using the Church of Everlasting Hope use a mace instead of staff as his preferred weapon, but only allowing him to casting his heal spells by bludgeoning his
Continuing on with the example:
Another player wants to focus on the Morrigan's death aspect. She picks a cleric from the Congregation of the Dead, which is NE in alignment. She see's the gawdess role as a necessary one and that dead should be a glorify part of life. She could do that but she could also pick the Cathedral of Light, which is LG, and still focus on the Death aspect.
Now remember that alignment is a meta-game concept. Even if she were to go NE, that would mean that she couldn't travel with a paladin of the Morrigan, or be shunned from society. Remember, at the end of the day, she still is a representative of her gawdess and deserves respect. Of course, she may have some theological disagreements with a Crow that uses the Cathedral of Light but that wouldn't always mean that they'd come to blows over it.
That also wouldn't mean that they wouldn't come to blows (after all, the Catholics and Protestants burned each other at the stake). It would simply be on a case by case basis.
