It all trickles down from the teaching that this skill is given to you by God, so you can do great things, but this other one over here is a punishment from God so you can atone through hard labor and suffering.
no it doesn't, the sister went off entirely on her own ruining her brother's reputation by calling him useless and a failure in front of everyone she ever met.
i do not disagree on the church causing persecution and misconceptions about unconventional skillsets, but the skills themselves are never a punishment in this manga, just the boon one receives through them differs greatly from individual to individual.
besides, chapters 9 and following specifically state that the discrimination a skill holder faces differs based on the arbitrary choices made by the church functionaries.
cyclo and mist were both discriminated against, yet their individual treatment differed from each other, while "heretic" caused outright persecution, "clockmaker" was disregarded as being of little value.
