The indigenous Christians regarded their faith as another path, as well as an upasana (worship) system of the Hindu mainstream. (PK Balakrishnan, Jati Vyavstituoum Kerala Caritravoum, Kottayam, 1983, p 345 ff). Thus it had not functioned as a distinct religion until the Synod of 1599. Even the names of the native Christians were Hindu such as Cathan, Kotha, Iravi, Kandan, and so on. (Thazhakadu Church Inscription of Chera King Rajasimha, 1028-1043 C.E). After the Portuguese arrival, a large-scale aggressive proselytizing movement started in Kerala under the stewardship of a padre called Francis Xavier. His eight-year stay in South India changed the entire course of its history. In a short period, he was able to enhance the numerical strength of India’s Christian population. He was not different from Mohammed Ghazni or Aurangazeb or Tipu Sultan in the space of proselytizing enterprise. Francis Xavier was the man solely responsible for the establishment of the Inquisition Court at Goa in 1560, under which Hindu women were raped and burnt alive and Hindu temples were demolished. (Kanayalal. M. Talreja, Holy Vedas and Holy Bible, New Delhi, 2000, p 170).
The wrath of the Catholic Church that was started by Francis Xavier in Goa did not spare even innocent children of Hindu origin. This Court of Inquisition functioned in Goa till 1812. Francis Xavier enjoyed all atrocities over Hindu population and thus remarked; “When I have finished baptizing the people, I order them to destroy the huts in which they keep their idols; and I have them break the statues of their idols into tiny pieces, since they are now Christians. I could never come to an end describing to you the great consolation which fills my soul when I see idols being destroyed by the hands of those who had been idolaters”. (From the Letters and Instructions of Francis Xavier, 1993, pp117-8 & V. Balakrishnan quotes from a letter of Francis Xavier to the Church authorities in Portugal as follows: “I told the new Christians to demolish the shrines of the idols and saw to it that they crushed the images into dust. I could not express to you the consolation it gave me to watch the idols being destroyed by the very hands of those who so recently used to worship them”. V. Balakrishnan, op cit, p 105 & Kanayalal M. Talrej, op cit, p 18). St. Francis Xavier, after whom many educational institutions are named in India with pride. What sort of pride is this? No doubt, Francis Xavier was a mentally debased fanatic or a bigot.
When I have finished baptizing the people, I order them to destroy the huts in which they keep their idols; and I have them break the statues of their idols into tiny pieces, since they are now Christians. I could never come to an end describing to you the great consolation which fills my soul when I see idols being destroyed by the hands of those who had been idolaters. St Francis Xavier
Later, he was elevated to the rank of Saint by the Catholic Church for his cruelties committed on the Hindu population of India, particularly of Kerala shore and Goa. His mass-conversion movement was targeted at the then socially low rankings of the society, such as the fishermen and the Dalits. It was because of the reason that he was concerned only about the numerical aspect of the Indian Christianity. In his task of proselytizing, he opted for the methods of coaxing, gift giving, persecution, etc. The aggressive evangelization programme opened by Francis Xavier some four hundred and sixty years ago created a strong base for Roman Catholic Church in India; the Christian population increased day by day and is now politically and economically a decisive factor not only in Kerala but at New Delhi also.
To do justice to the history of Christianity in India, it is essential to make an enquiry into the Church sponsored temple annihilations. The history of temple annihilation in Malabar Coast starts with Francis Xavier’s enterprises from the princely state of Travancore. In the Malabar regions it was quite late, during the time of Mysorean invasions. The first organized temple destruction of Kerala took place in the sixteenth century under the stewardship of Portuguese, who were the architects of Inquisition in Goa – the first Christian fanatics of the Orient. The initial prey of his dogmatic wrath was the temple at Thevalakkara in Quilon district and Palluruthi near Cochin. (T. K. Velupillai, The Travancore State Manual, Vol. II,  Trivandrum, rpt. 1996, pp 174,175 & A. Sreedharamenon, op cit, pp 228, 229). De Souza, the Portuguese governor, made a futile attempt to plunder the shrine at Thiruppathi is also to be remembered in this context. The same Christian forces, which claim tradition of Francis Xavier, set fire to of the famous Shasta Temple of Sabari Hills in 1950 May-June and later in 23rd March 1983 the same forces attempted to occupy the forest land by ‘planting a cross’ in the holy garden (grove) of the temple. The fertile Malayattoor Hills near the birthplace of Jagadh Guru Sankaracharya was occupied to construct a church initially by planting a cross in 1938. Subsequently they linked this place with St. Thomas legend. The Church occupied land still belongs to reserve forest category of Kerala. Under the Vote Bank politics of Kerala so far no competent authority challenged this encroachment of forest land. Unorganized Hindus of Kerala was then in helpless condition. So the Church endeavour at Malayattoor was an easy walkover. Further the organized Hindu forces defused foul stratagem of the Catholics to occupy a Hindu temple at Matrumala near Kottayam in the sixties of the last century.
Finally Portuguese came to terms with Travancore by which they agreed to abstain from cow slaughter in Travancore territory. (“In 1544 the Portuguese entered into a treaty with Travancore ……………….They on their side promised not to kill cows within the territory”. T. K. Velupillai, op cit, p 175.). It is important to consider the information available from the work of C. M. Augur, an English Missionary cum the Resident of Travancore, to pencil in a correct picture of the Christian intolerance from the days of Padre Francis Xavier to the generations of the contemporary church renovators. According to Augur in 1816 C.E there were, in the Travancore State (now the part of Kerala state), 19,524 temples and 301 churches for all denominations. But in 1891, that is after 76 years, the number of temples had come down to 9,364 and the number of churches had burgeoned to 1,116. (C. M. Augur, Church History of Travancore, Kottayam, 1902, pp 7, 8, 9). Another temple demolished by the Christian fanaticism during the assumed period was the Mahadevar Temple of Palayoor near Guruvayoor Temple. Until the days of the collapse of the disputed structure at Ayodhya, the Palayoor Church authorities kept a board in front of the church which reads: “The church was constructed by Saint Thomas after demolishing a temple”. (Now the board has been removed).
In short, most of the claimed eight churches of first century CE were located either on the ruins of the Hindu temples or near to celebrated temples. One such famous church was established in 1938 at Malayattoor, near Aaadi Sankara’s birthplace. It was earlier a Siva temple. The revenue records of the old princely state of Travancore concede this fact. The temple was known to the locality as “Kurinchimudi Temple” (hill peak temple). This hill region falls under the Kurinchi area of Sangam period topographical classification of Ainthinai (five tinais). After the Christian occupation in 1938 CE the name of the place was slightly changed to “Kurissumudi“ (Mount of Cross). During the Sangam period the entire South India was topographically divided into five regions (Ainthinai). The region contained hills and a mountain was called “Kurinchi“. That is from Kurinchimudi to Kurissumudi. Really the temple name was associated with its topography and was conveniently changed with the ‘sign of faith’ by the Christians after their occupation of the temple site. Considering the geographical area, the number of the temples set ablaze or knocked down in Travancore was proportionately much higher than that of temples demolished by the entire Muslim invaders/rulers of Northern India during the medieval period.
The Portuguese did not spare the Muslims of Malabar. The Sixteenth Century Muslim Arabic scholar of Kerala (Ponnani), Shaik Zainuddin, in his work Tuhafat-ul-Mujahiddin (A Gift to Deists), mentions their plunder and destruction of mosques. They did not spare the Kerala’s Jews either: to escape the Portuguese persecution, in 1565 the Jews of Crangannoor (at present Kodungalloor) escaped to places of Hindu dominancy such as Paravoor, Maala, Chennamangalam, Cochin (Kochi) and so forth.