It should be noted that, of all institutions, the Catholic Church engaged in what many scholars regard to be history's largest-scale social experiment in "negative eugenics" without actually killing or stigmatizing anyone (indeed, it went in tandem with a renewed focus on 'consent' and the right of spouses to choose partners without family involvement or paternal refusal).
This is no joke (its a huge often unspoken irony given that when involuntary euthanasia unfortunately returned in the 20th century the Catholic Church was (rightly) its most vocal opponent), and its widely recognised in scholarship that this was the first case of negative eugenics in the more benign way you describe, applied societal-wide:
Eugenics - Wikipedia
The first formal negative eugenics, that is a legal provision against the birth of allegedly inferior human beings, was promulgated in Western European culture by the Christian Council of Agde in 506, which forbade marriage between cousins.[15]
Pope Gregory I (540 – 604), writing after the Council of Agde, would note the following in a letter to an Englishman:
CHURCH FATHERS: Registrum Epistolarum, Book XI, Letter 64 (Gregory the Great)
Answer of the blessed pope Gregory: A certain earthly law in the Roman republic allows the son and daughter, whether of a brother and sister, or of two brothers, or of two sisters, to marry together. But we have learned by experience that the progeny of such marriages cannot thrive. And the sacred law forbids to uncover the nakedness of kindred. Whence it follows that only the third or fourth generations of believers may be lawfully joined together
William Durham has noted that this statement is evidence that the church prohibition was originally based on some recognition of the physical abnormalities and health problems that come from inbreeding.
Today, it is a huge social problem among people of certain nationalities because of traditional cultures like the Germanic one that the church changed through its social engineering consanguinity laws:
First cousin marriages in Pakistani communities leading to 'appalling' disabilities among children
Basically put, the medieval Church destroyed tribalism and heavily penalized its main vehicle - cousin marriage - through the strictest reproductive, consanguinity laws ever imposed on a population in the entirety of human history (I think it makes China's old 'one-child' policy look tame by comparison). This had very big ramifications as a form of social engineering, quite apart from removing some of the undesirable genetic traits that arise from inbreeding.
From Jack Goody’s “The Development of the Family and Marriage in Europe” [pgs. 56-8]:
“What were the grounds for these extensive prohibitions on consanguineous marriages? The ‘Dictionnaire de Droit Canonique’ (1949) gives three general reasons that have been proposed:
“1. The moral reason, that marriage would threaten the respect and shame due to near ones.
“2. The social reason, that distant marriages enlarge the range of social relations. This common ‘anthropological’ notion was put forward by those great theologians, St. Augustine and St. Thomas Aquinas, who recognised that out-marriage multiplied the ties of kinship and thus prevented villages from becoming ‘closed communities’, that is, solidary ones.
“3. The physiological reason, that the fertility of the mother or the health of the children might be endangered.
“The statements of Thomas Aquinas, which appeared in his ‘Summa Theologica‘ and was highly influential during the Middle Ages, raised a number of possible objections to consanguineous marriage…. (2 above)….
“1. The moral reason, that marriage would threaten the respect and shame due to near ones.
“2. The social reason, that distant marriages enlarge the range of social relations. This common ‘anthropological’ notion was put forward by those great theologians, St. Augustine and St. Thomas Aquinas, who recognised that out-marriage multiplied the ties of kinship and thus prevented villages from becoming ‘closed communities’, that is, solidary ones.
“3. The physiological reason, that the fertility of the mother or the health of the children might be endangered.
“The statements of Thomas Aquinas, which appeared in his ‘Summa Theologica‘ and was highly influential during the Middle Ages, raised a number of possible objections to consanguineous marriage…. (2 above)….
In the medieval period, marriage was prohibited by the Church at the Lateran Council of 1215 within the fourth degree of a consanguineous relationship, that is between third cousins or any anything closer.
But here's the thing: this all took place in a Christian social order that believed in fundamental human equality of status and soul, irrespective of hereditary illness or impairment (which is why the church had outlawed infanticide in the Roman Empire and other eugenic policies that went against basic human dignity).
There was no desire to 'eliminate' or leave to their fate the children of 'incestuous' unions, or to stigmatize them.
Again:
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.61.3711&rep=rep1&type=pdf
“The conquest of the Western Roman Empire by Germanic tribes during the medieval period probably strengthen the importance of kinship groups in Europe. Yet, the actions of the Church caused the nuclear family — constituting of husband and wife, children, and sometimes a handful of close relatives — to dominate Europe by the late medieval period.
“The medieval church instituted marriage laws and practices that undermined large kinship groups. From as early as the fourth century...It severely prohibited marriages among individuals of the same blood (consanguineous marriages), which had constituted a means to create and maintain kinship groups throughout history. The church also curtailed parents’ abilities to retain kinship ties through arranged marriages by prohibiting unions in which the bride didn’t explicitly agree to the union"
“The medieval church instituted marriage laws and practices that undermined large kinship groups. From as early as the fourth century...It severely prohibited marriages among individuals of the same blood (consanguineous marriages), which had constituted a means to create and maintain kinship groups throughout history. The church also curtailed parents’ abilities to retain kinship ties through arranged marriages by prohibiting unions in which the bride didn’t explicitly agree to the union"
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