The low-level violence I’m talking about has been constant background since the conquest, and more organized rebellion/military action were not uncommon throughout the colonial period. Some remoter corners of the continent took quite a while to conquer, and others were difficult to control.
To claim that colonial systems such as encommienda and repartimiento weren’t persistently violent is absurd: those Indians who tried to flee were killed; those who rebelled were killed; theft and destruction and rape and torture and murder were routine; local religious and cultural practices were suppressed; access to trade and credit were strictly controlled; indian peasants were treated as effectively slaves able to be forced into mining or construction projects or plantation work (with some weak checks and balances between groups of competing elites, particularly those who had been living there for a while vs. those newly arrived from Spain).
Historical analysis is hard work, and we have to read sources carefully, but there are a wide variety available including lots of material from colonial élites themselves (Severo Martínez Peláez’s La patria del criollo is, despite its flaws, quite an insightful deconstruction of one of these), and your suggestion that current scholars have just been naively deceived by “the Goebbels press” is disingenuous and offensive. As a good place to start, I recommend Murdo MacLeod’s book Spanish Central America: A Socioeconomic History, 1520-1720. (Further disclaimer: MacLeod is a family friend.)
Anyway, that’s enough about that for today. A last bit of friendly advice: I recommend you find a bit more empathy for people unlike yourself, tone down the hyperbolic rhetoric, and spend more effort on facts and explanations and less on speculation and judgment. When confronted with an author who flings expansive insults in all directions, I feel bored and alienated: it’s not worth wading through all the noise to look for whatever signal might lie within.