For the most part, I agree. Obviously it glosses over a lot and specific cases will vary.

You touch on what I think one of the biggest examples of this: the difference between how the Americas were colonized. In both cases, Catholic and Protestant, the colonization occurred. It was brutal, genocidal and one of the worst things to happen.

But at least in the Spanish/Catholic invasions, there was a real attempt at dealing with how to justify doing what they were doing to other peoples just as endowed by the creator with thought and reason. There were full out religious enclaves that helped or at least sheltered the native populations. Top thinkers in the Catholic Church back in Europe often came down against colonization and the interests of both the state and capital, creating a friction.

In North America, there was none of this. Almost everyone in protestant England was on board to just go whole hog taking over villages, land, killing, etc. The notable exceptions were the Catholic Irish, who were just getting over their own dealing with British Protestant colonization, and the French Jesuits, who wrote some of the better philosophical and anthological work of the period on the North American Native population.

Even this summary is obviously glossing over a lot of specifics, but I think it's pretty illustrative of how even compared to the relative evils of Catholicism, Protestantism is just on a whole separate level of justifying, if not outright supporting, atrocity.