IRC From my world religion & economics class there were two broad theological viewpoints regarding the New World. This is to give a basis on the actual thoughts of the Spanish at the time
The first was based on the beliefs of some Spanish humanists, which saw the heathens in a paternalistic manner. That the new world needed guidance and that the Spanish are the right people to do so. It fought against excesses such as extreme treatment of natives, enslavement of Christian converts, and so on. The focus was upon the faith of the humanists.
The second was the opportunistic interpretation of Catholic theology, which provided theological justification for the Spanish conquests. The assumption was that the Spanish were virtuous and that the natives not so much, why then did god endow the natives such wealth; obviously the answer is to attract the virtuous Spanish to lead them to the light. It was used to justify the enslavement, slaughter, of natives and also natives which converted. The focus was primarily upon the afterlife and maintaining the status-quo in the physical world to control the natives.
This is a gross oversimplification; there was a theological debate between paternal benevolence (still with a focus on conversion) and forced conversions, but it was very much a debate within the Catholic Church, rather than between humanism and theology.
Indeed, to the extent that it broke down into humanist vs. Church lines, it tended to go the other way; see the famous Valladolid debate between Las Casas, Bishop of Chiapas, who argued for the paternalistic position, vs. Sepulveda, the humanist scholar, who argued that natural law gave the Spanish the right and responsibility to use any means necessary to stamp out the "barbaric" practices of the natives.
It was often clergy like Las Casas who were the drivers behind the various Spanish laws aimed at banning the worst conquistador abuses; we rightly condemn De Landa for his destruction of native books and horrific inquisition in the Yucatan, but forget that a few years earlier he was criticized by the hacienderos as being far too sympathetic with the natives in his efforts to force the conquistadors to treat their charges humanely. Trying to paint a picture of "traditional religious bad/humanist good" is ignoring the fact that we are dealing with real individuals, with their own complicated beliefs and desires.
At the end of the day, the conquistadors were a very diverse lot of people (and remember that the conquest of the new world took centuries, with plenty of changes among them; the Spanish missionaries and soldiers trying to pacify the Seri in the 1700s came from a very different cultural background than the men who followed Cortez to Tenochtitlan). Describing them as a bunch of religious zealots motivated solely by fanaticism is as inaccurate as describing them as a bunch of cynical materialists out solely for profit. In truth, they were a mix of all sorts of motivations, with different levels of each among different individuals; trying to remove just one driver isn't likely to massively affect the overall picture.