Churches were not egalitarian organizations, Avernite. The concept of "equal" merely referred to the acknowledgment that the natives had souls. Not that they had, like, any rights at all to property, autonomy, respect, or choice.
The conversion efforts among primitive peoples intended to fill the bottommost rung of colonial society with obedient serfs and peons, so that the fruit of their labor could be first taxed by the state and the church, and then appropriated in full by the land owning castes. It had nothing at all to do with seeing these people as "equals" to anyone in a legal sense.
Missionaries might have frequently been emphatic people who cared about their flock's well being, but the church organizations and society at large really only had one place for converted darkies, and that was at the absolute bottom, below the lowest of the white Christians, with zero empathy given to their well being or their needs.
Now that's going in the other extreme, and just as wrong.
Having written what I just wrote in the previous post, I am now about to backtrack a bit.
First, to be clear, the "New Holland degeneration" thesis is fun because it exploded in British journals in the early 19th Century, and was seriously embraced and propounded in Anglican circles. But most of these were written by intellectual clerics who had never actually set foot in Australia themselves, indeed many had never even set foot outside of Oxbridge. The opinions and feelings among actual missionaries in the field, particularly long-term missionaries, is a lot trickier and harder to assess.
If you read journals of African missionaries, like David Livingstone, they have a much more respectful view of Africans and African society than their counterparts back in European scientific societies (albeit Livingstone's Scottish, not English, so maybe there's a thing there). I have never read journals of Australian missionaries, but I would be quite curious to see what they write.
But there is a precedent we can look at to guess what their feelings were: I point you to the American Jesuits.
The "New Holland degeneration" thesis is actually a late English variation on earlier French Enlightenment thesis on "American degeneration". This was not propounded not so much by churchmen, but rather by secular natural scientists. Remember, Montesequieu back in 1749 had connected character & moral qualities to climate and environment. This was a general view shared by many French natural scientists, and they especially applied it to the Americas. The French did not see savages as degenerating from a higher civilized state (like the Anglican thesis), but rather that they simply never evolved from an earlier state of nature to begin with.
The grandaddy of it all was probably George-Louis Leclerc Buffon (1747,
Histoire Naturel), who wrote an extensive natural history of the world, focusing most on "physical" characteristics of the animal kingdom. Buffon argued that because of America's environmental characteristics (wet, cold, marshy, etc.), the New World never developed large, aggressive land mammals like in the Old World, but only small and relatively harmless creatures. It took about five seconds for Buffon to extend that to humans. For the exact same environmental reasons, American Indian natives are also similarly "underdeveloped" humans - short, hairless, timid, not very virile (ergo the underpopulation of the continent).
"Underdevelopment" of physical characteristics was quickly extended to "underdevelopment" of intellectual and moral characteristics - American natives were childishly infantile, cowardly, weak, unmanly, etc. Buffon got the ball rolling, Montesquieu generalized it. Other French Enlightenment scientists ran with it to extremes. The "American underdevelopment" thesis was expounded in its most extreme form in Corneille Du Pauw (1768,
Recherches sur les Americains) and was popularized in Abbé Raynal (1770,
Deux Indes). There you will find some of the most paternalistic, racist derogations of American Indians ever written. Some, of course, like Jean-Jacques Rousseau, gave the twist of the "noble savage" - sounds a little better, but a savage nonetheless. Rousseau did not consider him a moral superior, but a moral nullity, kinda dull and stupid.
The "American underdevelopment" thesis even spilled over into Scottish Enlightenment writers, notably William Robertson's
History of America (1777), even though Scottish thinkers were generally disinclined to the environmental arguments found in their French counterparts.
Even Spanish writers, who really ought to know better, embraced this thesis. I mean, peninsular Spaniards were already prejudiced against their colonies generally - just a dumping ground for fortune-seekers and ne'er-do-wells. No civilized Spaniard would want to move there. The French Enlightenment writers just confirmed what they always suspected - America is a dump, a land for savages, unfit for civilization, never produced any, never will.
This "American underdevelopment" thesis was the height of Enlightenment science in late 18th Century Europe. It was also, you will notice, written by intellectuals who had never actually lived in America, or had any personal familiarity with Amerindians.
This was all corrected by missionaries.
Jesuit missionaries had been working in the Americas, among the natives, since the 16th Century. Then, all of a sudden, in the 1760s, the Jesuits were all ejected from their missions and deported back to Europe - Portugal had expelled them from her colonies in 1759, France in 1764, Spain in 1767. The former Jesuit missionaries were all unloaded at the Pope's doorstep in Italy. Upon their arrival, the former missionaries set about reading these "scientific" European works on America ... and rolled on the floor laughing. These Enlightenment guys knew
nothing about America. The speculations, the absurdities, the superiority complex, it was all laughable and ridiculous.
So, unemployed and with nothing else to do, the exiled Jesuits started writing real histories of America, to correct the record and improve European impressions of American Indians. There was a veritable stream of massive scholarly works by former Jesuit missionaries, pumped out after the 1770s through the early 1800s on natural, social and political history of the Americas, to combat the Enlightenment writers. It was these exiled Jesuit missionaries who wrote the great works expounding the virtues of American natives, often in the other extreme, as highly developed and advanced. They wrote down the histories and extolled the achievements of Pre-Columbian native civilizations - Aztecs, Incas, Toltecs, Mayas, Chimu, - as great or even superior to those of Europe. Aztec emperors were as great as Roman emperors, Texcoco was as glorious as Athens. And like Greek and Roman pagans, Mexicans "had always been Christians but didn't know it". American natives had a lot to be proud of, they weren't dull stupid savages, they were great innovators, industrious, great civilization builders, etc. Even relative backwaters like Canada and Chile got a makeover by Jesuit writers, placed on the same footing as European nations.
This had never been seen before. There was some awareness of Aztec, Incan, etc. civilization from the 16th Century chronicles of Spanish Conquistadors. But they focused on the conquest - adventure stories really. The Jesuit works instead went deep into pre-colonial history, and even in their colonial histories, focused on the Indian natives, not their colonial conquerors, and very much raised them as equals to Europeans. The absurdities of Buffon, Du Puaw, Raynal, etc. was just slanderous trash by ignorant Europeans, and the Jesuits assaulted their works line by line.
So I do want to correct the impression given above that missionaries were merely carrying out European prejudices abroad. Sure they had prejudices, and institutionally maybe too, back in the churches and mission societies back home. But on the ground, on the frontline, among the natives, the story was quite different. It was missionaries, more than anybody else, who learned to actually admire the natives, not merely to protect them, and endeavored to correct the paternalistic, derogatory view of them back in Europe.
So take their civilizing role with caution. Yes, the missionaries brought clothes, workshops, schools, etc. and other accoutrements of European civilization that infringed on native life. Was that bad? It is well known missionaries had a very relaxed attitude towards natives and their lifestyles, it is there if they want it, or they can take it in partial measures. Livingstone famously only made one convert in thirty years. He wasn't exactly very heavy-handed.
The missionaries weren't the authors of laws or enforcers of them - the colonial authorities were. If natives were forced into mission schools, it is not because the missionaries wanted them to, it is because the colonial governments wanted them to. Mission schools, raised by private donations, happened to be the only schools around - colonial government sure as hell was not going to expend state money building anything for natives. The missions happened to be there, and the colonial governments decided to use them to impose government will.
In sum: I don't actually know what Australian missionaries thought. The "New Holland degeneration" thesis is intellectual speculations written by Anglican scholars back in England. If the Jesuit example is anything to go by, I wouldn't be surprised if actual missionaries in Australia had a very different opinion.