In The Pioneers by James Fenimore Cooper, how do we reconcile Natty’s objections to the town folks actions with the spread of modernization?

Natty, who looks back at a time when the wilderness around him was more pristine and pioneers far sparser, deplores the careless, wasteful, and irresponsible ways the new influx of white settlers domesticate nature. At the end, however, having received the governor's pardon, he does reconcile himself to the changes in two ways. First, when looking with Oliver and Elizabeth at the graves of the Major and Mohegan, Natty notes that much will be reconciled in heaven after they all die. Natty says the following:

There is One greater than all, who’ll bring the just together, at His own time, and who’ll whiten the skin of a blackamoor, and place him on a footing with princes.

Then, Natty tells Elizabeth and Oliver that he is moving onward, westward:

They tell me that on the big lakes there’s the best of hunting, and a great range without a white man on it unless it may be one like myself. I’m weary of living in clearings, and where the hammer is sounding in my ears from sunrise to sundown. And though I’m much bound to ye both, children—I wouldn’t say it if It was not true—I crave to go into the woods agin—I do".

Natty realizes and accepts that he cannot do more to impact the change that has come. Though Elizabeth protests that he is too old to live in the wilderness, he argues that he "craves" it. It is what he wants, and he says that he will die at peace in nature.
Natty does not completely object to the civilizing of nature, but he has done his part and has spoken his piece in favor of moderation and conservation, promoting a balance between human need and the needs of the wilderness. He attaches moral significance to moderation. As he says to the Judge much earlier on,

It is much better to kill only such you want, without wasting your powder and lead, then to be firing into God’s creatures in such a wicked manner.

Elizabeth accepts that it is Natty's nature to wander on the edges of civilization, in the areas that are yet unspoiled, just as he accepts the inevitability that New York will be changed by white society. Natty can leave with some assurance that he will not be forgotten by Elizabeth and Oliver and that, through them, some of his wisdom retained. The novel ends with Natty heading onward:

He had gone far toward the setting sun—the foremost in that band of pioneers who are opening the way for the march of the nation across the continent.

It is worth noting that Cooper envisions white society spreading west: Natty is not so much escaping white civilization as forging the path of its destiny. Natty may have deep misgivings about settlers who are naive or who deplete the rich resources of the land, but he also accepts the inevitability of their spread.