"I'm really not comfortable comparing the human sacrifices of the Aztecs to the sweeping massacres led by the Pilgrims and Puritans. First of all, the motivations and the ultimate results were vastly different."
I would say they are directly parallel -- except the human sacrifices of the Aztecs continued for a longer period of time and occurred on a much larger scale. Religious justification for conquest of neighboring areas is pretty parallel...
"Additionally, history hasn't been written to hide the human sacrifices."
Out of curiosity -- will you be discussing the eastern tribes tendency to the ritualized torture of war captives (both Native American and white) with your kids while discussing Bradford? That's something that's not discussed when we talk about Thanksgiving either.
"I am really uncomfortable with the "everything in it's historical period" analysis. While I don't think you can ignore historical context, I do think it often provides a very comfortable way to excuse things that happened in the past, as "oh, but that's what everyone did then". "
Its not an excuse -- its trying to understand the motivations and actions from the framework in which they arose. I do not, in any way shape or form, disagree that the conquest of the Pequot was wrong. However, I am very uncomfortable with a historical analysis that looks back 400 or 500 years, imposes 2008 values on whites and then basically doesn't hold other racial/ethnic groups to the same standards. It seems to imply that only the "white folks" could be expected to know "better".
"During colonization there were articulate critics and resisters to the genocide both white and native, and I believe this to be true of virtually every struggle we have record of, there are always dissenters."
I agree that is true, and that it is frequently the people who can essentially see further than others that are the "great men/women" of history. I guess I don't agree that they are as common as you seem to think, especially when you look at a world without TV, telephones, internet, regular newspapers, radio or mechanized transportation. The community that any one Pilgrim would have interacted with regularly was very, very small and so the chance of hearing dissenting opinions was also small.