The problem with labelling something as "good" or "evil" is that it requires a particular moral viewpoint. decisions about what is good or evil are value judgements, and are highly subjective depending on one's value structures.
In order for a religion to flourish, it needs to have an internally consistent system of morals and values. This was something that I had to deal with squarely when I was the Morgath coordinator for the HRT back in the day, and it was what led me to write the article on Practical Morgathianism
. Whether you believe in the underlying tenets of a particular belief system has a lot to do with how you judge the values espoused by that system. To the die-hard Morgathian, the kind of order imposed by a Laranian world-view would be anathema. Even, dare I say, evil. To a die-hard Laranian, the human-sacrifice component of Morgathianism alone would put it in the evil category.
Where you run into trouble is in looking at the underlying tenets of religion or belief, namely that these assumptions and beliefs are by their very nature unprovable. Hence, they must be taken on faith. Whether you think someone is a madman or a prophet largely hinges on whether or not you believe what they are saying is true.
Anders Breivik believed that he was performing a vitally important act in protection of the Norwegian people, and that someday they would thank him. We reject this belief as delusional, as we have rejected the rationales of other serial killers (like David Berkowitz, the "Son of Sam" killer who heard voices that he attributed to god).
But in the Harnic milieu, I think this problem actually becomes more profound simply because of the profusion of different "socially acceptable" styles of belief. In a setting where the gods are real and supernatural forces abound, it becomes much more difficult to dismiss these beliefs as delusional. You might demonize them, or claim that they are the work of forces anathema to your own belief system, but claims of supernatural involvement are much more likely to be given credence. And if the "delusional" belief system becomes widespread, who is to say that it's false? Balsha was considered little better than a rabble-rousing madman by Corani authorities, and as a heretic by the very Morgathians whose belief system he popularized. Yet his legacy endured, and even worked its way into the Morgathian orthodoxy.
Similarly, you have the "Cult of the Midnight Dancer" in Moleryn. This cult, mentioned in canon as possibly a form of debased Navehanism, could very much be the legacy of one deranged individual who managed to attract a small audience. And in a world where the supernatural is demonstrably real, I would think that it would be easier to gain followers simply because people's belief systems are already open to the idea that there are a wide variety of divine beings out there.
And this sort of fringe belief system need not be confined to the "dark" churches. I could very much see a serial killer with a very devout Peonian belief system who poisons his victims, all of whom he believes are sick and living in severe physical (or even spiritual) pain. He may see himself as doing them a favor by ending their suffering painlessly. Is his belief delusional? Are his actions "evil?" It all depends on whether the premises upon which he's basing his actions are factually right or wrong, which is usually something that's impossible to determine.
To me, this has always been the greatest strength of the Harnic pantheon - whatever you think of the gods themselves, it describes institutions that are very human, and by extension lie open to just the kinds of interesting moral dilemmas, conflicts, flukes, and oddities that make for good role-playing. The first time my players met a sympathetic Morgathian NPC, it sort of threw them for a loop. In my Lia Kavair campaign, several of the players like dealing with the Agrikans because they always know where they stand.