I don't think it's ever been implied that there's any kind of supernatural brainwashing involved when it comes to the heretics. They sympethize with the dragons of their own free will.
Or, at least, some of them do. Now that they're meddling about with Primals, it's possible that the Heretics have developed the ability to temper folks even when Iceheart isn't Shiva, just as the beastmen can temper folks without the direct presence of their Primal. Even so, Shiva is a recent creation, so if the heretics ARE using tempering to swell their ranks, that is a recent development. Prior to that, all heretics were there by choice.
We haven't seen much of the story from the Heretics' point of view. To the Ishgardians, the Heretics are wretched betrayers of humanity, siding with the monstrous dragons who must all be slain at all costs. The Ishgardians don't seem to know or care WHY the Heretics have sided with the dragons. Knowing the Heretics' reasons will be a key indicator of how sympethetic they're meant to be. Do they side with the dragons because they're aware of Ishgard's "sin" and know that the dragons are in the right? Do they side with the dragons because they are tired of centuries of war, they believe the dragons will win in the end, and so they want to bring the war to a close as soon as possible? Do they admire and covet the power of dragons, and side with them in the hopes of gaining personal power?
