Native Americans did not plan to keep their population in check.
Multiple causes of death and the complete lack of technology impaired their ability to significantly increase in population.
Lack of the wheel and draft animals made it difficult to bring more land under cultivation.
Less food equals less people.
They did not choose this situation as some sort of moral imperative.
The aboriginal cultures of several Latin American countries actually managed to ruin their environment.
The would denude surrounding hills for firewood and cause cataclysmic erosion.
Don't view the Native American as a noble savage.