As to the comment above - are you suggesting the Spanish deliberately spread diseases? It seems a little unfair to accuse the Spanish invaders of bio-warfare.
the inquisition &etc were as much about cultural conformity and control than about espousing a culture of violence. while ridiculous the question is not to compare ridiculousness levels but to compare the _reasons_ that people were doing the ridiculous things they did.
killing people for the express and explicit purpose of killing people is bad mojo.
They shouldn't have done it...
..at least by our standards today. It is always difficult to judge historical people because we are, even from an early age, in possession of more facts than they were.
You're actually right, there's little evidence or even mention of biological warfare until much later, and truly only in the North American field. However, bio-warfare likely dates back at least three-thousand years, so it would be hard to tell.
Furthermore the Spanish didn't really need biological warfare, "for with fifty men one could keep the whole population in subjection and make them do whatever one wanted." However, given that the Spanish had some of the harshest policies on forced labor, it's not hard to see why they wouldn't want to use biological warfare. The encomienda system offered protection to tribe members in exchange for tribute through labour, this didn't effect tribes like the Incas where they had a system like this long established, but for the Arawak it is thought to be why they ended up with large populations on the south american mainland.
I think the Spanish deliberately chose not to spread disease so as to make the most profit, which is easy to see considering Spain basically took on the policy of strip-mining south America to send every ounce of gold they found back to Spain.
Given that most native populations at the time had nothing more than bronze-age technology, they couldn't even take a stand against the Spanish. The Spanish in their war with the Incas managed to kill easily ten times their amount of men, but there's few reports of Spanish casualties in their fights against thousands of natives. In many battles they achieved 400:1 ratios of Indian:Spanish deaths in battle.
Consider that at the Battle of Thermopylae the Spartans only managed 10:1, despite the home-turf advantage, better tactics, land advantage and far superior training as they were fighting against a largely conscripted army. Considering the Spanish achieved a 40-fold increase in advantage, it shows how unbelievably powerful steel armour, muskets and cannon were. Not to mention the Spanish made extensive use of horses.