C'mon, Doug, give the guy a break. He's not trying to absolve the colonists and early Americans for their crimes against native americans, which are obviously ghastly in any case. The point is to try and understand what really happened, to get at the truth.
How is asking these questions any different from Chomsky and Herman's study of the Cambodian genocide, and their refutation of claims of 2-3 million killed by Pol Pot? They don't deny the fact that lots of people were killed, only that western claims were inflated. They were not trying to defend the Khmer Rouge either - they were simply trying to discover the truth of what happened in Cambodia under Pol Pot, and use these facts to expose the bias in the US media.
I admit that these 2 situations are different in the sense that Chomsky and Herman's work tends to undermine the coercive institutions in their own country, while this sort of scholarship with respect to the genocide of native americans tends to make western colonialism (and presumably by inference current western society) look better than an accusation of outright premeditated genocide. So at best you could decry a more detailed study of the native american genocide as somewhat irresponsible.
But, as "Bhodi" pointed out in his initial post, most people already agree that what happened to native americans was tragic and awful (especially on this list), so its hard to say that it could be used as an apology for the real crimes that were committed.
To a large extent plagues suffered by native americans were NOT the fault of the colonists. Even if you assume that the colonists had been "good neighbors" to the indigenous population, you would STILL predict this sort of thing to happen. European populations were densely populated and geographically concentrated, which over time leads to greater immunity (and exposure to a greater number of potentially nasty microbes) in the general population.
In contrast, native american tribes were sparse and geographically dispersed, and therefore had not been exposed to pathogens as regularly and didn't have as high an immunity as the Europeans. Contact among the two populations was bound to lead to plauges among the native americans, regardless of whether the colonists were friendly or hostile.
Again, I'm specifically addressing the issue of disease as a factor in reducing the native american population. The numerous cases of massacres and theft and destruction of resources that took place should be denounced as horrible, indefensible crimes. But someone who tries to determine, as objectively as possible, the facts of the situation shouldn't be denounced for it (although they could be criticized for other reasons, i.e., shoddy scholarship, etc.)