(Based on Niall Ferguson's Empire) The British East India Company had a strict policy against encouraging Christian prosetlyization. They presciently feared that such efforts would interfere with their aim to extract the maximum rent from the Indian economy. After the evangelical success in demolishing the Atlantic Slave trade, however, those evangelicals could not be persuaded to forbear any longer, and an intense parliamentary campaign culminated in orders to let in and support the missionaries.
Their forthright goals were to save the Indians from their benighted religion and bring them the blessing of Christianity and Capitalism. Their passion was particularly aroused by three Indian practices they found extremely offensive: female infanticide, thagi (quasi-religious associations of murderers and thieves), and suttee (or burning widows alive on their husband's funeral pyres). If they had confined their attentions to these, Indian resentment might have been manageable - since they all had plenty of Indian critics as well. But their ambition was far more grandiose - to turn Indians into English Anglicans.
The resulting resentment, and others provided explosive fuel for the Rebellion of 1857. The spark was the issuance of a new type of rifle cartridge sealed with pig or beef fat, the ends of which needed to be bitten off - anathema to Hindu and Muslim. The soldiers rebelled, killed their white officers, and went on a rampage, slaughtering every European or Christian they encountered. Horrible atrocities were committed, and women and children were chopped to pieces by the rebel soldiers.
Many consider this the first Indian war for independence, but it never had unified leadership or much by way of goals besides slaughtering foreigners. When word of the rebellion and atrocities reached London, the rage was intense. The same evangelicals who had wept for the slaves and victims of infanticide now wanted blood, and oceans of it. The retribution was terrible. Whole cities were slaughtered, and rebels were hung by the thousands, blasted by cannons or just shot or bayoneted.
It was the end of the East India Company, but the Royal authorities who replaced them resolved to keep close control of future missionaries.
Religion - Christian, Hindu, and Muslim - had once again proven its efficacy in promoting mass slaughter.