I agree completely with the previous response. We often take for granted that religion has to lead to intolerance and bigotry. If we drop that assumption (pretty hard to do, as we live in the real world) perhaps it is possible to imagine that established religion could provide a moral foundation for the behavior of heads of state like Danforth. It is a bit of reach to argue from this position, because by definition, established religion is intolerant and arrogant, but I think it's about as close as we can get to a way to attack the question.
Maybe we can argue, in the case of The Crucible, that authorities should maintain a firm understanding of a community's moral code. When judges like Danforth refuse to pardon innocent people for the sole reason that others have already been put to death, they erase any moral standing they once had and effectively ignore the moral calling which initiated the trials in the first place.
If Danforth had considered the morality of his situation, which can be symbolized by the Church, maybe he would have found humility, forgiveness, and contrition instead of the injustice and hubris which he achieves.