That played a large role, but they were also pretty far behind Europe in military technology so I am almost certain they would have been conquered anyway. It would have just taken longer.
I'm no expert in the matter, but from what I've read it seems to me that the Mesoamerican civilizations in 1492 were probably at about the military level that the Eurasian civilizations had already reached in the first millenium BC.
I agree that if the disease luck had gone the other way and a large fraction of Europe had died of disease then it's possible the Native Americans would have remained unconquered. If the disease factor was just taken out of the equation completely, I think the Native Americans would have been conquered, simply because of the great European advantage in technology. But the conquest would have looked more like England's colonization of India, and many more of the native cultures would probably have had a chance to evolve and assimilate modern technology, like India's cultures did, rather than just going extinct.
There's some speculation that Syphilis may have been a new world plague. The first major outbreak was a couple of years after Columbus returned, but figuring out when the first ever case was has proven more difficult.
It’s impossible to tell. If it had taken decades or a century longer because their numbers were higher, they might have had time to start up their own production of technology.
I think the thing to consider isn't really if the conquering of the Americas to some degree wouldn't have happened, but if a larger population would have changed or slowed the interactions between Europe and the Americas in various ways.
I'm no expert in the matter, but from what I've read it seems to me that the Mesoamerican civilizations in 1492 were probably at about the military level that the Eurasian civilizations had already reached in the first millenium BC.