One thing I ask these writers to contemplate is that heresy is in the eye of the beholder.This is certainly true in history. The Pharisees considered Jesus Christ a heretic, but for reasons of their own did not want to deal with Him as such under Jewish law.
In the history of the early Christian Church, also, the “heresy hat” traded hands a lot over the centuries. In the fourth century, for example, the Arians and Athanasians took turns wearing it.
In more recent times, the Báb and Baha’u'llah were considered heretics against Islam, but obviously the six or seven million Bahá’ís in the world don’t regard them in that light.
This informs the way I write my fiction. The protagonists of The Meri trilogy (Book View Cafe 2012) were considered heretics by the religious institutions they challenged. Both the orthodox religionists and the “reformers” (Taminists) considered themselves to be true to the common scripture they both used — although the orthodoxy depended a great deal on tradition and commentaries written through the ages by scholars. The Taminists considered these commentaries to be man-made accretions, the orthodoxy viewed the new revelation the Taminists followed to be heretical.
In The Spirit Gate (Baen 1996), which explored an alternate history Poland (Polia) in the 1400’s, I had the Holy Frankish Empire, the Teutonic Order, the Islamic Turks and the pagan Poles and Mongols meeting in a war of wills, weapons, and magic in which Polia was the prize.
My Frankish bishop was the worst sort of heretic — he was destroying his own faith and its institutions from the inside, blindly driven by his own desire for spiritual power. His rationale was Machiavellian — the ends (ridding Polia of pagan and heathen influences) justify the means (a dangerous form of “twilight” magic, in this case). But I portrayed him sympathetically in the sense that there were those who felt his strong-arm tactics were exactly what was needed, and he believed he was doing the right thing. So, too, did his pagan antagonist, who was also willing to ignore the teachings of his own religion in order to further ends he felt were justified.
The most important thing, I think, is to let the characters’ behavior do the talking. Rather than rendering judgement as narrator (which is often done through the use of adjectives—”the sly priest”, “the noble cleric”) or through having characters speechify about the evils of the “other”, set forth some real behavior and let the reader decide if a character is sly or noble.