Disease was the biggest killer, and, as you said, sooner or later the Europeans were going to arrive. Without resistance to those diseases from Europe and Asia the Native Americans were in serious trouble, even if the Europeans had arrived with the most peaceful of intentions.
True disease was the largest killer of native Americans fought by their exposure to the Europeans.
But in all reality the intensions of the Europeans was not conquest but trade. The original intensions of the Europeans was trade in furs at first and then tobacco.
Even with Cortez the original purpose of his mission was trade. But when Montezuma sacrificed 200 men in front of he and his men in a single day he decided that this was not a man that could be dealt with but a diabolical creature that must be stopped.
But in today’s society Christian values, a historical perspective of men and their times is not is not permitted in a polite discourse of issues dealing with the races