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.

Around 90% of the people died of plagues.

It's really impossible to speculate how things would have progressed without those plagues.

Or worse, if Native Americans were full of plagues that the conquistadors would bring back to Europe to cull 90% of Eurasia.

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.