In his book “The Mission of God” (Wilberforce Publications, London 2016), the author Joseph Boot quotes Darwin. On page 381 of that book, he introduces the quote thus:

On his world voyage on the HMS Beagle, Charles Darwin, despite his growing agnosticism and deistic religious confusion, found himself unable to overlook the profound impact of Christian missionaries in Tahiti and the Pacific Islands. In the first work he ever wrote, before the implications of his theory gripped and ruled him, Darwin’s Christianized background caused him to rain praise on the evangelical missionary.

There follows this quote, which, according to the endnote, is from

Charles Darwin: Journal of a voyage round the world (London: T. Nelson and Sons, Paternoster Row, 1890), 496-947.

This is it:

It appears to me that the morality and religion of the inhabitants are highly creditable. There are many who attack … both the missionaries, their system, and the effects produced by it. Such reasoners never compare the present state with that of the Island only twenty years ago, nor even with that of Europe at this day; but they compare it with the high standard of gospel perfection … [T]hey forget, or will not remember, that human sacrifices, and the power of an idolatrous priesthood – a system of profligacy unparalleled in any other part of the world – infanticide, a consequence of that system – bloody wars, where the conquerors spared neither women nor children – that all these have been abolished, and that dishonesty, intemperance, and licentiousness have been greatly reduced, by the introduction of Christianity. In a voyager to forget these things is base ingratitude; for should he chance to be at the point of shipwreck on some unknown coast, he will most devoutly pray that the lesson of the missionary may have extended thus far … [T]hose who are most severe should consider how much of the morality of the women in Europe is owing to the system early impressed by mothers on their daughters, and how much in each individual case to the precepts of religion. But it is useless to argue against such reasoners; – I believe that, disappointed in not finding the field of licentiousness quite so open as formally, they will not give credit to a morality which they do not wish to practice, or to a religion which they undervalue, if not despise.