The Church has, throughout its history, been often cast as a usurper. Within our thinking we see ourselves as blessed, righteous, champions, savior of souls; but to those around us we can seem to be bullies or pawns of the State and in fact can be both is our blindness and sinfulness.
Roque and his companions were martyred because they championed Christ among the tribes of Brazil and championed the human rights of these tribes against the ruling States that wanted to control them(one of which was his own brother - who apparently reneged after Roque's harsh words to him). The Jesuits of the time were assailed from all sided, mainly by the jealous both in European and tribal leaders. At the time the Spanish conquistadors were brutalizing and enslaving the local indigenous people of South America, even though the pope had declared them off-limits. Similar to attempts by missionaries in California, Roque and his companions successfully worked to make them self-sufficient and free by gathering them into groups. Though I could find no source for it, it is said that years later, even Voltaire - a true hater of Jesuits - praised them for their effort (he does have Candid go and "fight for the Jesuits" (Chapter 14) before killing one).
We have to keep all that in mind, even though we are in every corner of the world. Missionary work is not about winning territory, but about winning souls for Christ and bringing Christ's dignity to all, regardless of religious or political affiliation. We must speak truth to power for the sake of the Kingdom.
I have received your letter and understand from it and other letters the strong feeling and complaints you have regarding the Indians and especially the feelings you have against us.
This is nothing new nor anything that started yesterday. The encomendero gentlemen and soldiers have long complained and even gone further by stirring up strong opposition to the Society of Jesus.
This is, in fact, a great honor to us.
I say this because the cause of the Indians is so just and because they have and have had a right to be free from the harsh slavery and forced labor called personal service. Indeed, they are exempt from this by natural law, both divine and human.
These complaints grew even more serious after members of the Society fulfilled their obligation as faithful ministers of God and vassals of his majesty the King and supported what he order most justly through his visitor that the Indians should be free from servitude in which they were kept.
-- From a letter to his brother Francesco, lieutenant governor of Asuncion
Things to Think About