I will share with you some of the conclusions that I have reached:
1. The arrival of the Europeans in all of the Americas (in the case of the Spanish: Cuba, Peru, Mexico, the Rio de La Plata region in South America, Florida, Texas, New Mexico, Baja and Alta California) relatively quickly led to the destruction of an admirable and balanced way of life. Many will argue this was inevitable.
2. The Spanish colonized Alta California in a relatively humane and Christian way, and the Native Americans were treated better in the early decades than they were in many other Spanish and European dominated territories.
3. From the Franciscan perspective the missions led to the baptism and conversion of thousands of Native Americans, and for the Catholic believers, that consequence overshadows all other end results.
4. A careful study of the Native American reaction to the mission life leads to the inescapable conclusion that some of the neophytes were satisfied with their lives, were truly converted and embraced the "better way" presented to them; and others hated the highly regimented life in the mission communities and wanted to return to their original way of life. In some missions 10-15% of the neophytes tried to escape in a given year.
5. Over the years of Spanish and (after 1821) Mexican approach to the Native Americans changed. In the later decades of the mission era the soldiers were more aggressive in hunting down Indians and forcing them into the missions. There were more revolts by neophytes.
6. The situation varied by mission, largely based on the personality and leadership of the senior padre. In missions like San Luis Rey, under Fr. Peyri, the Indians were well treated, run-a-ways were less of a problem and the mission achieved great success. San Luis Rey had the largest neophyte population in all of the Americas.
7. A comparison of how the Native Americans were treated by the Spanish with how they were treated after the American takeover of California and the “Gold Rush” days is revealing. The relatively few surviving Indians in the 1840s and 1850s were treated much more cruelly by the Americans who coveted their land and distrusted the natives.
I hope these insights stimulate your thinking. The “civilization” that took place in the late 18th and the 19th century – all over the world – led to destruction of a way of life and rapid declines in native populations (largely due to the introduction of “European” diseases like Smallpox to which the Natives were not immune). The Spanish colonization led to the creation of a Spanish speaking, Christian population in the Americas that is vibrant, growing and proud of its unique heritage.