Yes but the disease and resulting depopulation was probably a necessary precondition to European settlement nonetheless. Even as it was, European settlers themselves often assimilated into indigenous communities; this is the most likely explanation for the lost colony of Roanoke, and smaller scale instances of this sort of thing were well-known late enough that Benjamin Franklin wrote about the phenomenon. Without disease and depopulation, there would have likely been no good uncontested sites to colonize in the first place, and the American Indians would have likely been able to resist colonization far more effectively.
At any rate, there’s no generalization to be made either way. In some cases, conquest involves an existing population accepting foreign rule; in other cases, it involves population replacement. Even counting which cases count which way is difficult and controversial.