I suppose if one says it enough times others will come to believe it to be truth. Nothing can be further from the truth about Fray Serra killing Native Americans. In fact, documents support that Serra protected the Native Americans in both Mexico and Alta California against policies that if enacted by the Viceroy would have would have resulted in adverse outcomes for the Native Americans. Fray Serra was never personally responsible for the execution of any Native American. It is sadly true that with the arrival of Europeans a byproduct was that the Natives were not immune to viruses and disease that caused their near extinction. But if not the Spaniards, then the Russians or Americans from the east would eventually have the same affect.
The arrival of Europeans carrying often fatal diseases certainly hastened the population loss in Alta California as it did throughout the Americas when Europeans encountered Native Americans in any context. The high death tolls in Missions have been examined by scholars and findings showed several major diseases took terrible tolls and accounted for the massive population loss rather than murders or executions. Many children died in a major measles epidemic in 1805 for example. It was brought into Monterey by an infected ship's crew and spread to Los Angeles in less than 3 months. Other death tolls and illnesses can be attributed to change in diet. Father Serra's diary notes confusion as to the spread of dysentery when he adds more protein to the local diet at Carmel by giving out lots of milk....Yet it was not known until the 1940's that Native Americans lack the enzyme lactase that breaks down the lactose in milk. Hence they become sick as the lactose ferments in the stomach and digestive tract. So yes, Serra's act of sharing milk may have had adverse health implications. He hastily sent the sick people back to home villages for their usual diet and they got well. So this hardly resulted in a paved road of skulls. Not just roads, but highways could be formed however, with the bones of those who died from diseases introduced unwittingly by any contact with Europeans.
Franciscans, such as Fr. Ripoll at Santa Barbara during the 1824 Chumash Revolt, wrote lengthy letters to the government in Mexico complaining about the shooting of several unarmed Chumash and calling for solders to be prosecuted for murder. The sad death toll is too easily dismissed as a deliberate slaughter when the Spanish government had a vested interest in Native survival due to the lack of Hispanic population at the time who were available to become citizens who would help keep the Russians out of California.
In defense of the Spanish peoples led by Fr. Serra, it should be noted that Spanish colonialism viewed Native people as citizens while English settled areas did not grant such citizenship rights to Native Americans until 1924 in the United States. Under both Spain and Mexico, Native Californians had defined and extensive legal rights. That does not condone colonialism but acknowledges the reality of the world exploration and contacts increasing in the 15th through 19th centuries. Isolation became impossible. It is an unfortunate tragedy that so many Native Californians died of diseases. Of great concern is when people condone death tolls that could have been avoided. After the Americans arrived in California, it became legal, in 1850, to kill Natives "on sight" as they were considered always hostile so such killings were always self-defense not murder. That horrendous lack of civil protections led to a population loss of 70% between the 1850 and 1860 census of California. The life of Native Californians since the arrival of Europeans has been disastrous. To blame the violence and death tolls on Fr. Serra however is a somewhat unfair and limited view of history.
Walker, Phillip L. , and John R> Johnson.2003. For everything there is a season: Chumash Indian Births, Marriages and Deaths at the Alta California Missions. In Ann Herring and Alan Swedlund (eds.), Human Biology in the Archives. Cambridge: Cambridge University Press pp.53-77
Geiger, Maynard. 1970. "Fray Antonio Ripoll's Description of the Chumash Revolt at Santa Barbara in 1824,"Southern California Quarterly 54:345-364.
Blackburn, Thomas C. 1975. "The Chumash Revolt of 1824:A Native Account," The Journal of California Anthropology 2:223-227
Tac, Pablo. 2001 [1830s]. "Indian Life at San Luis Rey." In Rose Marie Beebe and Robert Senkewicz (eds.), Lands of Promise and Despair: Chronicles of Early California, 1535-1846. Berkeley: Heyday Books. Pp.329-340.
Heizer, Robert F. 1978. "treaties" In Robert F. Heizer (ed.), Handbook of North American Indians. Washington D.C.: Smithsonian Institution, pp.701-704.
Haley, Brian and Larry Wilcoxen. 1997. "Anthropology and the Making of Chumash Tradition." Current Anthropology 35:761-794.