Viewing the blood-red paint splashed on the St. Junípero Serra statue decapitated in the wee hours of Sept. 10-11 brought to life in my mind a small, but telling incident in Serra’s life.

Serra had crossed the border between Baja and Alta California on his epochal journey in 1769 and was just shy of San Diego, what would become the first of 21 Alta California missions. Of course, Serra saw no border because there wasn’t one. The Californias, north and south, were united for 10,000 years under hundreds of Native American tribes, and the Kumeyaay populated what today straddles American and Mexican territory.

The military head of the Spanish expedition, Gaspar de Portola, spotted what Serra called “good, sweet water” in a deep ravine, probably in today’s Tijuana River National Estuarine Reserve.

Portola thought the pool a great place to drink, water the horses and mules, wash clothes and bathe. Serra’s response was surprising. After chiding Portola for wanting a second drink on the same day, he stopped everyone in their tracks, “We do not want to spoil the watering place for the poor gentiles.”

Does that sound like a man guilty of genocide?

Serra went all the way to Mexico City from Carmel on foot and mule to get the military commander of California sacked for not removing soldiers who were molesting and raping Indian women. 

He graphically told the Viceroy, “The soldiers, clever as they are at lassoing cows and mules, would catch an Indian woman with their lassos to become prey to their unbridled lust. At times some Indian men would try to defend their wives, only to be shot down with bullets.” 

When the Kumeyaay revolted in 1775 and burned Mission San Diego to the ground, killing three Spaniards, including a priest friend of Serra’s who had treated them with great care, Serra insisted to the Viceroy that those imprisoned and waiting execution be released and forgiven. The Viceroy cashiered Commander Fages and he ordered the Kumeyaay released, as per Serra’s insistent wishes.

The Mission Santa Barbara vandalism of Sept. 11 is being investigated by the FBI as a hate crime. Over the past two years, similar incidents have happened at four other missions: Carmel, San Gabriel, Santa Cruz and San Fernando.

At Mass the Sunday after the Serra statue decapitation, Franciscan Father Larry Gosselin, associate pastor of St. Barbara parish, reflected on the Gospel message about forgiveness. “Christ took it to the infinite level — you can’t stop forgiving, especially if you want forgiveness yourself,” he told parishioners, “We have no animosity for the perpetrators.”

No one has been apprehended for the vandalism and the Franciscans emphasize that no one knows who did it or why or what community, if any, they are from. Nevertheless, Father Gosselin said something Serraesque: “This is an opportunity of grace. Facing the whole thing in the spirit of forgiveness, no blame is given.” 

He drew an analogy to the forgiveness in person of Pope John Paul II of the would-be assassin who shot him. He even imagined a scene where Franciscans might meet the vandals of the Serra statue in jail and walk out with them together. “Maybe we would all be changed,” he smiled.

This smacks of Serra himself, who once told the Viceroy if he himself were killed by the Indians, no one should be punished.

The anticolonialism argument that grew in the 1980s and culminated in wholesale protests at the Columbus quincentenary in 1992 is still compelling: European powers brought unparalleled suffering and death to the indigenous peoples they encountered in conquering the New World for their empires. This is a plain and shameful fact. But it is not simple.

Reading more than 60 comments to an story on the Santa Barbara Serra statue decapitation, it also becomes clear that the anger poured on the Serra image issues not only from anger over the suffering Native Americans have been visited over centuries, but also another matter entirely — the pedophilia scandal that has rocked the Catholic Church and other institutions (notably the Boys and Girls Scouts). 

Having said all that, I discovered over time that Serra, though far from perfect, was different. Like the Dominican Bartolome de las Casas, who in 1552 published perhaps the earliest document expressing outrage over colonialism, “A Short Account of the Destruction of the Indies,” the Franciscan Serra was a brave advocate of the indigenous: opposing colonial overlords, ministering to California tribes he thought better Christians than the Spaniards, constantly clashing with the Spanish military, chiding the Spanish governor of California, Felipe de Neve, for refusing to refer to Indians as “gente de razon” (people of reason).

Still, the accusations of enslavement, torture and even genocide persist concerning the Franciscans in California. Again, some of this is displaced spleen against other serious but unrelated issues, as well as a disinterest in actually looking at who Serra was, and some of it is simply a misreading of history. 

Perhaps it would help if we looked at what happened in California in three distinct stages (which critics erroneously elide). The first stage is Serra’s advent in 1769. California was one of the last untouched places Europeans encountered in the New World. And by then, at least by ministers like Serra, something had been learned.

Serra almost never referred to Indians as “barbaros,” a common appellation at the early years of the conquest of the Aztec and Inca. Serra would usually say “indios” or “gentiles.” He saw the Indians as having an inviolate soul with a connection with the Creator as important, and perhaps more important due to their vulnerability, as any European. 

More than once Serra referred to the California Indians as living “in their own country.” Needless to say, conquistadors don’t speak like that.

Under Serra, it is simply inaccurate to say Indians were enslaved. They came into the missions of their own volition. Did they understand the bargain they had made? Some did, some did not. 

At a time of great confusion and upheaval, especially at the appearance of epidemics no one could stop, they were given food, shelter, work, even pay, an environment of art and music, but they were to live with a “communitarian spirit,” as historian Douglas Monroy puts it, a sort of indentured servitude. That meant they could not leave without permission. They were part of a small, isolated working community that depended on them for life itself. Most took the common annual leave. But punishment by whippings caused some to flee — perfectly understandable. What is truly surprising is the estimated fugitive rate: 5 to 10 percent. If conditions were so horrible, why did at least 90 percent stay?

There is no gainsaying the floggings, of course. They were wrong. Serra should have been as enlightened about corporal punishment as he was about so many other things.

As for the second and third stages of colonial conquest of California, life under Serra’s Franciscan successor, Fermin Lasuen, was decidedly not enlightened. Lasuen was something of a racist. Some Indians began to be forced into the mission and military forays to capture runaways become more common. 

The third stage — the advent of the Americans in 1848 sparked by the Gold Rush — was out-and-out genocide. The rate of decline of the Indian population in California tripled under the Americans. The American cavalry hounded Indian tribes, forced displacement and expulsion was plainspoken as a policy by the first American governor. 

Emeritus professor of history at Cal Poly San Luis Obispo Daniel Krieger asks pointedly, “What would the experience of Native Americans under United States control have been had there been a man with Serra’s unflagging energies trying to restrain a President Andrew Jackson or General Philip Sheridan?”

Serra was simply head and shoulders above Lasuen and the American juggernaut. There’s a reason Serra is named a saint and Lasuen is not.

Whoever cut the bronze head off that Mission Santa Barbara statue had no idea who Serra was. They got the wrong guy.

Gregory Orfalea is author of “Journey to the Sun: Junípero Serra’s Dream and the Founding of California” (Scribner, 2014), and the children’s book “Junípero Serra and the California Missions” (2015). He is working on a novel about baseball and Syria.