Enforced Method Acting: In the earliest episodes, Daniel Knauf intentionally kept Clancy Brown in the dark about whether his character was supposed to be the Creature of Darkness or the Creature of Light. In interviews, Brown has admitted that he initially thought it was the latter, as he thought Brother Justin's visions were proof that he was some kind of messiah (just like Brother Justin himself did). Though he eventually caught on, it made Brown's performance as a Knight Templar that much more believable at the beginning, as he genuinely thought that he might be playing the hero.
Executive Meddling: Lots. As Clancy Brown has put it, HBO was "uncomfortable with ambiguity," and so altered story-lines and characters to fit their needs. Brother Justin becoming all but pure evil in the second season in contrast to being conflicted in the first was because of this. Scenes where Justin was depicted as being more sympathetic were vetoed by the producers. HBO meddled quite a bit with Justin and Iris' relationship. They pushed for Justin to rape her at the end of the first season (which the writers did not want to do, hence the ambiguity of that scene), and then demanded that the show drop their relationship entirely in the second season.