He discouraged vaccinations because disease was a natural means of population control.
Thomas Malthus worried that the amount of resources ( such as food and water) in the world would not be able to keep up with the increasing number of population in the world.
He believed that diseases are natures'ways of population control to ensure that the resources is enough to accommodate all organisms in the world. Because of this, he believe vaccinations as interference of the natural order.
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The central idea is that the white people are worse than natives insofar that it may seem like the Natives are brutal savages, but it is actually the colonists who are worse because they "poison the heart" while the natives only "scalp". He explains that he tried and failed and is sorry that soon the Natives will be just like the White men. Expand this into two paragraphs and add a bit more quotes.