Why did Jesuits and Franciscans disagree about indigenous labor in their missions? Alejandro Murguía in "The Medicine of Memory" wrote that Jesuit missions in New Spain were averse to controlling native labor. When Franciscans and Dominicans took over after the expulsion of the Jesuits, their missions did rely on the compelled labor of missionized natives.

What was the theological(?) disagreement between Jesuits and Franciscans that led to their diametrical policies with regard to native labor?
The reason the Dominicans and Franciscans were allowed to fill the void when the Jesuits were expelled (and subsequent rebellions put down) was because the Bourbons had taken over rule of Spain from the Hapsburgs in 1700.  The Bourbons hated the Jesuits, but encouraged the other religious orders who filled the void.
&quot;The Medicine of Memory&quot; appears to be about the Missions in California, rather than the ones in Mexico and South America.  St. Junipero Serra gets a bad rap from Indian activists around the time of his canonization; he even received a decapitation.  But there, he didn't take over for the Jesuits. There simply were no Spaniards in the area, there was no military to enforce Californian natives to build missions until 1776 (that year seems important).
When St. Junipero died in 1784 there were &quot;4,500 Indians living in missions&quot;.  If at that point things started to go awry, it more likely attests to the degradation in treatment of the native populations in the second generation to the normal decay of things when a popular and respected leader passes from this world with no clear plan of succession (not unlike St. Francis himself).  It takes a while for things to sort themselves out. (For a modern parallel, when Tito died, Yugoslavia went to the dogs).
Nevertheless:

the Spanish government never authorized Indians to be bought and sold, as were the Blacks of Africa.  The Indians were treated as persons, not property
Christ and the Americas, Ch 4

The best argument against the underpinning argument that the Franciscans, and even the Spaniards, were not unjust in their governing was that

for 300 years, during which time Spain governed the New World without professional soldiers or standing military forces, except in a few places on the frontier to protect against raids from uncivilized tribes
ibid.

The book Christ and the Americas says that the denigration of the Spanish achievements in the Americas was due to The Black Legend, an early form of Fake News.   Oddly enough, it was a Dominican, Servant of God Bartolemeo de las Casas, who first spread the word about abuses.  Doubly odd, he is already venerated as a Saint in the Episcopal and Lutheran Church.  Not to cast too many aspersions,  but it would seem that the very same anti-Catholic, anti-Spanish sentiment that prompted the English and the Dutch to promulgate propaganda would extend to the memory of the good Bishop.