Plague Wardens
Plague Wardens believe the central duty of a Shallyan is to protect as many people as possible from the plagues and pestilences pervading the Old World. Rather than treating the victims, they aim to stop the plagues from spreading and creating victims in the first place. Their goal is noble; it is their methods that make them fanatics.
The only way to stop a plague is to destroy the source of the infection. That may mean killing someone with the plague, and then burning the body and boiling the ashes. It might also mean razing a whole section of a town, burning it down while trapping the doomed inhabitants inside. Plague Wardens recognise these acts are unpleasant, but feel they are justified by the greater good.
As Plague Wardens kill people, it goes without saying they are considered dangerous, and worse, by most members of Shallya's cult. Shallyan priestesses who join the cult almost always have difficulty casting spells, due to repeatedly breaking the central stricture of the faith. Plague Wardens see this as a test imposed by their Goddess, to ensure their faith is strong.
While Plague Wardens are violent zealots, they do believe they are acting to save people's lives. Thus, they do not kill on mere suspicion of infection, and all groups of Plague Wardens include at least one person with diagnostic abilities. These abilities are not always very good, but Plague Wardens only kill when they are fairly sure plague is present. They are also among the most implacable adversaries of the Fly Lord, and if they uncover evidence of a group of his cultists, they ignore all their other plans to concentrate on eliminating the greater threat.
Ironically, it is quite likely that the Plague Wardens actually have saved thousands more lives than they have ended. While their membership is very secret, their existence is well known to the educated, and they are a favourite example when priests of Verena discuss ethical dilemmas.
The Suffering Hearts
Shallyan doctrine is suspicious of personal pleasure in a world filled with so much suffering. The Suffering Hearts take this suspicion to an extreme. They are followers of Karin the Pure, a priestess who lived in Nuln a little over two centuries ago, and believed Priestesses of Shallya had to purify themselves of the taint of pleasure and luxury before they could properly minister to the suffering. Attempting to do so while impure was, she claimed, blasphemous.
While Karin was, eventually, cast out by the cult for denouncing the entire hierarchy as blasphemers against Shallya, her followers remain in mainstream temples, and keep their places by moderating their strictures against others. This also gives them more time to inflict suffering on themselves. Minimal food, little sleep, and inadequate protection from the elements are the basic elements of the life of a Suffering Heart. Most believe deliberately inflicting injuries on oneself is an affront to Shallya, so instead they take on hard and dangerous tasks, such as carrying heavy stones up to the top of the temple buildings, and then back down again.
The Suffering Hearts do nothing to relieve the pain of others, because they follow Karin's belief that it would be blasphemous to do so before they have been purified. Some Suffering Hearts do see visions that they take to be signs from the Goddess that they have been purified, and these individuals start to help. The proportion of miracle-workers among them, while not high, is higher than among other priestesses. Others, however, never feel pure enough, and as a result the cult hierarchy tries to discourage these beliefs. The Goddess of Mercy, however, cannot condone harsh measures against people who are merely misguided followers.
The Suffering Hearts are not a sect, as they have no internal organisation, and their interpretations of Karin's beliefs can vary a great deal. Indeed, this sort of belief has been present in the Shallyan faith for centuries, and Karin's particular version has little sway outside the Empire.