There were big differences between the secular and mission systems in California, particularly insofar as regulating the behavior of the soldiers was concerned. So for you to lump these two administrations together is in this case unfair. For the most part, most of the damage to the tribes that the Franciscans did was due to cluelessness.
As to overt genocide, the Americans who came to California were worse to the Indians than the Spanish ever thought of being.
I’m looking at the bottom line, pretty well know that the Nazis were responsible for the death of 6 million jews. The Spanish , in N. and S. America were responsible for way more than that. I’ve seen estimate of up to 70 million but the number vary but no matter , the end tally is way more that 6 million . They’re motto was kill the indian to save his soul. So I lump.