What If Catholic Monks Led First Expeditions to the Americas Instead of Columbus?

  Possibly if you had some sort of warrior monk culture still about, such as the Templar's or the Teutonic Order?  Although if so why would they seek to cross the Atlantic?  Columbus was driven by a desire for glory/wealth and a belief that the distance to China and the far east was much shorter than it actually was - which meant it was only saved from disaster because the Americas were in the way.  Contrary to common myth the main opposition to the idea wasn't that the 'learned' thought the world was flat but that they had a more accurate understanding about the actual size of the world.

  Assorted clerics were in the Americas very quickly after their discovery and had big impacts good and bad on the population that.  They were of course eager to erase the 'pagan' religions and often did much to destroy traces of it.  However they also at times sought to protect the local population against abuse by their new rulers, which is a major factor in the beginnings of the trans-Atlantic slave trade as the Spanish monarchy were persuaded that the Americans should be protected but that black slaves purchased from Africa could be used for the brutal work that they wanted the natives protected from.  [Although I don't think many blacks were used in the brutal silver mines in the Andes which was among the worst on the continent. 

  As I've mentioned before it probably wouldn't make much difference because the invaders, with rare exceptions didn't deliberately spread disease, had little capacity to and had no reason to.  It was only really in the settler colonies in the north that was a possible useful tactic.  Also other ruling invading cultures wouldn't have been significantly [if any] less brutal than the Spanish and other later colonisers were.

  Very likely.  Although I'm not sure how they would have treated converts?  Still with a level of contempt/mistrust or more accepting?

  I did actually plough through the video, including your standard denials but facts are somewhat limited.  Its about 3 minutes inside a 10 minute video before you even start talking about your assumption and then in an inaccurate way.

a)  Columbus's 1st expedition wasn't some sort of massive invasion force but three ships, two very small, which were sent to find a way to China.  Later missions might have had different purposes but until his last years he is supposed to have believed he was still on the verges of China and the Far East, which would make militarily centred missions unlikely.  It took quite a while before it became clear that the lands found were both huge and not part of E Asia.

b)  Yes the Spanish court did pass laws to protect the native populations against abuse and they were sometimes effective, hence the importation of slaves from Africa to replace workers in the Spanish Caribbean.  [Along with of course that the locals were often dying in devastating numbers so a labour force needed to be imported].  However as far as I'm aware the bulk of the labour forces for the big estates and the mines were from the same local native groups.  There is zero chance that such laws would be passed until Spain knew a lot more about the new lands and also they had them firmly under their control and at least nominally converted to Christianity.

c)  Spain was an intolerant country when it came to religion, in part because of the totalitarian bias of the Abrahamic faiths, in part because of the long wars to drive the Muslims back out of Spain and in part because centralised control is often favoured  by those in power.  Its unlikely that religious orders would have been any more tolerant and probably less, until the natives were all converted to Christianity and their traditional beliefs suppressed.  Which as you can tell from history wouldn't have happened without a lot of bloodshed.

d)  Your idea that the mass deaths from disease only occurred decades later as a deliberate policy and in large part as a result of forced starvation of the population doesn't fit the facts on numerous points.

i)  Large scale deaths from disease were inevitable because of the much large disease pool of the old world and the small level of genetic diversity in the new.  For instance the biggest long term killers will probably malaria and yellow fever, which were totally unknown in the Americas until they were accidentally introduced by people from the old world.  This introduction was definitely NOT deliberate as the people at the time didn't know enough about their transmission and since those disease, once established also killed many of the colonists it would have been doubly stupid.

ii)  There are numerous accounts of widespread epidemics within years of 1942, with Aztec opposition to the Spanish being greatly reduced by the massive death toll that occurred before Cortes's army was able to return to Tenochtitlan with their new allies and similarly the Incas were being hit by plagues before the Spanish even reached them.  Also the reports of early explorers in the Amazon of the large settled populations there confused later ones who found massive depopulation which seems to have been the result of the accidental introduction of disease by that group passing through.  Similar problems appear to have developed, although not quite as devastating with early Spanish explorers in what's now the US SE region.

iii)  As I've pointed out before it makes no sense at all to seek to exterminate people if you want to them to work your farms, mines etc or pay taxes.  Such policies only make sense - ignoring for the moment morality - if your interested in the land to settle your own people on.  That's why deliberate genocide would make no sense outside those places where the intent is to introduce your own people as the only/majority population.  Its noticeable that the Spanish empire fell at least in part because 'pure'-blood' Spanish whether locally born or from Spain formed only a small part of the population of the American empire.  So I very much doubt that, after the initial states opposing Spanish rule were crushed there was such an intent inside the Spanish Empire.  What became the US is a different matter because it did have such an attitude and i fear that once established unless this could be curtailed the forced expulsion of the natives - such as with the 5 'civilised' tribes could have been avoided.   However across most of the rest of the Americas this doesn't seem to be the case.  [Definitely there were 'racial' biases and discrimination but that doesn't seem to have been the cause of the vast bulk of the deaths and nor do most seem to have been intentional].

e)  You are aware that the Knights Templar wouldn't have been an option for one of your orders?  Apart from their reputation for religious intolerance they were destroyed about two centuries before 1942.