The people were charged because it was a criminal case. Had it been a civil action, they would have gone after the company. Pretty sure it's the same in the US.

Take a look south of the US border sometime. Most of the Central and South American population is of native descent. Of the ones that died, most didn't "chose" to, but died of imported diseases no one really had control over. The only large area of the Americas where natives were completely eradicated was North America, which happens to be the only area colonized largely by non-Catholic nations...