Some people have been called to severe mortifications. St. Catherine was one of them. She did this not from mental illness, but from a love of God and an obedience to God that helped her to reach the heights of mystical union that God called her to.
St. Paul teaches us that we are to be masters over our bodies and over our passions. This is the very definition of mortification. We all are to mortify ourselves in some way, that is, to bring into subjection our bodies and passions. Jesus also taught that we are to mortify ourselves. (see Romans 8:13; Colossians 3:5; Galatians 5:34; Luke 10:13; Matthew 11:21)
The Church, however, discourages severe corporal mortifications unless one is under the wise counsel of a Spiritual Director who knows about such things. One reason the Church takes caution about this is precisely because of severe mortifications resulting from mental illness. Such mortifications must come from an interior conversion (as stated in the above quote) and not from any mental defect.
In terms of your analogy of the body as a temple, actually, the Temple of Solomon was hammered and tempered through fire (in terms of the the metals). Even the woods must be cut, chiseled, and formed, and sometimes put through a firing process. This is the image of mortification.
But, make no mistake, no person should ever perform severe mortifications, not even a hair shirt, without the guidance and approval of a spiritual director.
Pain as an integral part of human nature united to Christ
Theologians also state that the Son, the second person of the Trinity, united himself as a person (through the hypostatic union) to everything human, including pain.
Catholics believe that God, who in their view by his divine nature cannot change, has united with changing human nature, and therefore with human pain. The "I" of the Second Person suffers and feels pain. He is one with pain through Jesus Christ. Thus Christ's experience of pain (like all the human acts of Christ like sleeping, crying, speaking) whose subject is the divine Person is an infinite act. This is based on the classic dictum that the acts belong to the Person (actiones sunt suppositorum). It is the Person who acts: It is God who walks, God who talks, God who is killed, and God who is in pain. Thus a Christian who is united to Jesus Christ through pain is one with his infinite act of saving the world.
This also goes together with another dictum in theology: whatever is not united (to the Divine Person) is not saved. Thus, his intellect, his will, his feelings, are all united with the Person, and are all sanctified and redeemed, including pain. Pain is therefore a sanctified and redeeming human experience.
The teaching of Pope John Paul II: the salvific meaning of suffering
John Paul II, who himself was known to practice flagellation sometimes along with other penitential practices like sleeping on a floor and extensive fasting (from a book about his canonization process presented by his cause's postulator; John Paul often did it before important events like ordinations), wrote an entire Apostolic Letter on the topic of suffering, specifically the salvific meaning of suffering: Salvifici Doloris. It is considered a major contribution to the theology of pain and suffering.
He wrote this after suffering from a bullet wound due to the assassination attempt of Ali Agca. Six weeks after meeting his attacker, he wrote about suffering in Christianity.
"Christ did not conceal from his listeners the need for suffering. He said very clearly: "If any man would come after me... let him take up his cross daily, and before his disciples he placed demands of a moral nature that can only be fulfilled on condition that they should "deny themselves". The way that leads to the Kingdom of heaven is "hard and narrow", and Christ contrasts it to the "wide and easy" way that "leads to destruction." Christ does not explain in the abstract the reasons for suffering, but he states: "Follow me!". Come! Take part through your suffering in this work of saving the world, a salvation achieved through my suffering! Through my Cross. Gradually, as the individual takes up his cross, spiritually uniting himself to the Cross of Christ, the salvific meaning of suffering is revealed before him. ...It is then that man finds in his suffering interior peace and even spiritual joy."
Joy in suffering: sharing in the redemption
Saint Paul speaks of such joy in the Letter to the Colossians: "I rejoice in my sufferings for your sake". One interpretation of this has been to think that he found a source of joy in overcoming the sense of the uselessness of suffering. Generally, however, the scholarly consensus is not that he rejoices in the "sense" of purpose in suffering, but rather in the help its ends brings to others. A balanced view is thus that he did not enjoy the suffering nor condone unnecessary suffering, but was simply more concerned with the good of others than his own well being.
It is sometimes thought that faith in sharing in the suffering of Christ brings with it the interior certainty that the suffering person "completes what is lacking in Christ's afflictions" (Colossians 1:24); this is often misinterpreted to involve a certainty that in the spiritual dimension of the work of Redemption he is serving, like Christ, the salvation of his brothers and sisters. Rather, the meaning is more obvious. His suffering did, on his missions, authenticate the gospel to those whom he was preaching. It is not as if they contributed to anyone's salvation, except in the external sense that they demonstrated the strength of his conviction and sincerity.
The need for prudence
The Desert Fathers emphasize that mortification is a means, not an end. They generally recommended prudence when practicing mortification, with severe mortifications done only under the guidance of an experienced spiritual director. Consequently, practicing mortification for physical pleasure is seen as a sin. Likewise, mortification for reasons of scrupulosity (which is similar to obsessive-compulsive disorder) is considered very harmful: a contemporary example is fasting due to anorexia nervosa. Catholic moral theologians recommend that the scrupulous not practice mortification, avoid persons and materials of an ascetical nature, and receive frequent spiritual direction and psychological help. Not all forms of self-mortification are approved of by the Catholic Church. Practices such as the nonlethal crucifixions performed on Good Friday in the Philippines are generally frowned upon by Catholic officials. Participants imitate various parts of the Passion of Christ, including his crucifixion. The spectacle draws a large amount of tourism every year.
The teaching of Benedict XVI
Cardinal Joseph Ratzinger who later became Benedict XVI told Peter Seewald in God and the world:
"When we know that the way of love — this exodus, this going out of oneself — is the true way by which man becomes human, then we also understand that suffering is the process through which we mature. Anyone who has inwardly accepted suffering becomes more mature and more understanding of others, becomes more human. Anyone who has consistently avoided suffering does not understand other people; he becomes hard and selfish. Love itself is a passion, something we endure. In love I experience first a happiness, a general feeling of happiness. Yet, on the other hand, I am taken out of my comfortable tranquility and have to let myself be reshaped. If we say that suffering is the inner side of love, we then also understand by it is so important to learn how to suffer — and why, conversely, the avoidance of suffering renders someone unfit to cope with life."
He also said in the Way of the Cross:
"In sinking to the depths he rose to the heights. Now he has radically fulfilled the commandment of love, he has completed the offering of himself, and in this way he is now the revelation of the true God, the God who is love. Now we know who God is. Now we know what true kingship is. Jesus prays Psalm 22, which begins with the words: "My God, my God, why have you forsaken me?" (Ps 22:2). He takes to himself the whole suffering people of Israel, all of suffering humanity, the drama of God's darkness, and he makes God present in the very place where he seems definitively vanquished and absent. The Cross of Jesus is a cosmic event. The world is darkened, when the Son of God is given up to death. The earth trembles. And on the Cross, the Church of the Gentiles is born. The Roman centurion understands this, and acknowledges Jesus as the Son of God. From the Cross he triumphs ever anew."
Cardinal Ratzinger states that pain, the very product of evil and sin, is used by God to negate evil and sin. He states that by freely suffering the pains that went with his passion and death on the cross, the Jesus fully reveals his love, making up for Adam's and mankind's sin, and makes man grow into maturity.
I hope this helps to understand mortification.