One of the earliest leaders of the church, Nicolaus, was called out in the Apocalypse of St. John with a warning that those who follow his guidance will find themselves opposed by Jesus. He said he would come against them with the “sword” of his mouth (that is, justice):
So you also have some who hold the teaching of the Nicolaitans. Repent then. If not, I will come to you soon and war against them with the sword of my mouth. (Rev. 2:15-16 RSV).
Nicolaus was chosen by the Apostles to be one of the first seven deacons of the church. At the time of his ordination, he seemed to be good and just man filled with the Holy Spirit:
And the twelve summoned the body of the disciples and said, “It is not right that we should give up preaching the word of God to serve tables. Therefore, brethren, pick out from among you seven men of good repute, full of the Spirit and of wisdom, whom we may appoint to this duty. But we will devote ourselves to prayer and to the ministry of the word.” And what they said pleased the whole multitude, and they chose Stephen, a man full of faith and of the Holy Spirit, and Philip, and Prochorus, and Nicanor, and Timon, and Parmenas, and Nicolaus, a proselyte of Antioch. (Acts 6: 2-5 RSV).
What went wrong? What exactly was Nicolaus being criticized for in the Apocalypse? We can find some clues in early Christian writers. St. Irenaeus suggested it was because of immoral behavior:
The Nicolaitan had as teacher Nicolas, one of the seven who were first to be ordained by the apostles. They lived unbridled lives. What sort of people they are is fully exposed by the Apocalypse of John, for they assert that there is no difference between committing fornication and eating food sacrificed to idols. 
St. Isidore of Seville, following further cues handed down to him from tradition (with writings we no longer possess), went further and said that Nicolaus abandoned his wife, giving her over to others who wanted to be with her:
The Nicolaites (Nicolaita) are so called from Nicholas, deacon of the church of Jerusalem, who, along with Stephen and others, was ordained by Peter. He abandoned his wife because of her beauty so that whoever wanted to might enjoy her; the practice turned into debauchery, with partners being exchanged in turn. 
St. Clement of Alexandria was not sure if Nicolaus, or those claiming to be his followers, were at fault; he believed Nicolaus was a strict ascetic who came to abhor the flesh.Yet, he affirmed that the Nicolaitans believed that Nicolaus had given up his wife to anyone who wanted to be with her. In either occasion, the flesh was abhorred, and it was as a result of ascetic ideals that an inversion of morality became permitted, where the abhorrence of the flesh was shown through sexual promiscuity instead of chastity. But yet, reading the story further, whether or not Nicolaus was guilty of what those who followed after him claimed, what was promoted in his name was not only abhorrent, but a form of ritual sexual abuse. His wife was said to be abused as a way to abuse the flesh. Whether or not Nicolaus personally guilty and had did what was claimed as Irenaeus and Isidore thought, or his ideas were misappropriated by his followers as Clement suggested, the problem remains: the Nicolaitans represent an early case of sexual abuse within church history. Women were seen as the “flesh” which was to be given up and over to anyone who wanted to abuse them; this abuse was rightfully condemned in the Apocalypse with no uncertain term. It was to be hated, and hating such abuse is something good (not because hatred itself is good, but because opposing evil actions is):
Remember then from what you have fallen, repent and do the works you did at first. If not, I will come to you and remove your lampstand from its place, unless you repent. Yet this you have, you hate the works of the Nicolaitans, which I also hate. (Rev. 2:5-6 RSV).
Seeing the connection between Nicolaus and sexual abuse, it is clear that sexual abuse has been in the church from the beginning. It has also been condemned from the beginning. But it remains with us and like the poor, it will be with us to the end of time. This is not to say when we find it, we should do nothing. No. Just like the poor need our help, so those abused by members of the church need our help; just as the rich who are capable of helping the poor are judged for their despicable behavior and condemned for their lack of charity, so the clergy are to be judged and condemned for the harm they do. When clerical abuse is not prevented but remains unpunished, then it should not be surprising, as in the case of the Nicolaitans, further forms of debauchery emerges and becomes proclaimed as something good.
St. Peter Damian, who saw widespread clerical abuse in his time, with bishops and priests thinking their authority permitted them to do whatever they wanted, wrote considerably against such abuse, demanding whoever was shown to use authority as a means to engage such abuse to be sufficiently punished. Writing to Pope Nicholas II, Peter Damian indicated the fate of those who will not justly punish such abuse:
He who failed to discipline his subjects must rightly suffer punishment from the supreme judge, and will deservedly be exposed to the lion “that prowls around looking for someone to devour,” since by his sloth an inertia he failed to impose salutary penance. 
The story of Phinehas in Scripture, he said, indicated the blessings which is to occur by those who meet out just punishments:
What we are to understand in all this if not the fact that the crime of adultery committed by eminent people must be more harshly punished? And he who is aroused to punish such men doubtless wins peace from the heavenly judge, and grace, not only for himself, but also for the people.
Sometimes, priests were rightfully condemned. But it was more important to look to the bishops. If they were lax, they too deserved condemnation. Peter Damian said it was absurd when their crimes were ignored:
For we indeed punish acts of impurity performed by priests in the lower ranks, but with bishops, we pay our reverence with silent tolerance, which is totally absurd. 
The history of the church shows that many ecclesial authorities have committed abhorrent crimes. To ignore the deficits of the bishops, to ignore the crimes of the clergy, to ignore the way innocent, good people have suffered at the hands of church officials might make for a form of apologetics, but it harms any authentic attempt to understand church history and the reality of the evil which is found side by side with the good. The holiness of the church is related to the grace of God; there are many who cooperate with it and become one with it and so emerge holy. Others, however, abuse it as they harm fellow Christians, and in that way, they are still a part of the church, and we must recognize the harm that they have done and continue to do as being a problem for the church. Hans Urs von Balthasar was right in his Casta Meretrix to say we must look to the evil within the church and not ignore it if we want to truly understand what the holiness of the church means when we talk about it being holy:
Do the Old Testament’s words about the archwhore Jerusalem have any kind of application in the New? Can any theological idea concerning the old people of God, especially one as important and central as this, be written off as totally redundant and irrelevant to the New, of historical interest only? Convinced that it was impossible to deal with the matter in this way, Erich Przywara developed his passionate “Theology of the Hour”, which he called “Covenant Old and New”. In what follows we want to do something much more modest. We shall assemble some of the material (by no means all of it!) from the theological Tradition that shows how strongly the great theologians felt that this idea was still relevant to the New Testament. Ours is a purely historical undertaking. We intend, without prejudgment, by critical examination and in temperate language, to set out the most important themes. It will then be for the theologians to draw their conclusions. They should do this calmly, and yet not so anxiously that, by maneuvering and making subtle distinctions, they empty the whole thing of content and render it harmless. Without endangering the immaculateness, holiness, and infallibility of the Church, one must look the other reality in the eye and not exclude it from consideration. Much would be gained if Christians learned more and more to realize at what price the holiness of the Church has been purchased.
The holiness of the church comes from grace. The holiness of the church is the holiness of Christ. That holiness will be realized in the eschaton as the church is purified of all the evil. It is a shallow sense of holiness which makes us think that the grace of holy orders turns clergy into super-heroes; they are not. Many do great evil. The holiness of the church remains. It remains because the church subsists in the institutional church, so it is to be found in the institutional church as grace is shared and received by its members. But there will remain those who have received grace and who will abuse it, using it for their personal gain instead of properly interacting with it and using it for personal transformation and holiness. When they are discovered, we should not hide them from public view, preventing them from receiving just condemnation. When we find out that some are hidden out of shame, or for some worse motive, then those who are responsible for covering up such abuse must also be judged. It is vital for the church, to be true to itself and its mission, that such injustice is called out and rejected. “It is essential that we, as a Church, be able to acknowledge and condemn, with sorrow and shame, the atrocities perpetrated by consecrated persons, clerics, and all those entrusted with the mission of watching over and caring for those most vulnerable.” This must be done. For we are to be the salt of the earth, but if the salt has lost its saltiness, that is, the church has lost its engagement with holiness, we shall find ourselves rightfully condemned not only by society but by the justice of the divine judge himself.
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 St. Irenaeus, Against Heresies Book I. trans. Dominic J. Unger and John J. Dillon (New York: Newman Press, 1992), 90-91.
 St. Isidore of Seville, The Etymologies. Trans. Stephen A. Barney, W.J. Lewis, J.A. Bach and Oliver Berghof (Cambridge: Cambridge University Press, 2010), 175.
 See St. Clement of Alexandria, The Stromata Books One to Three. Trans. John Ferguson (Washington, DC: CUA Press, 1991), 234 [II.118(3)].
 See St. Clement of Alexandria, The Stromata Books One to Three, 272 [III.25(6)].
 St. Peter Damian, “Letter 61” in The Letters of Peter Damian 61 – 90. Trans. Owen J. Blum, OFM (Washington, DC: CUA Press, 1992). 13.
 St. Peter Damian, “Letter 61” 5-6.
 St. Peter Damian, “Letter 61,” 4.
 Hans Urs von Balthasar, “Casta Meretrix” in Explorations in Theology II: Spouse of the Word. Trans. John Saward (San Francisco: Ignatius Press,1991), 197-8.
 Cf. Lumen Gentium 8.
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