The reason they're not dressed up as natives:
#1, the game is not meant to be perfectly historically accurate, and explaining something like that takes away from the pace and adds little to the story.
#2, it's an animated painting, and in the paintings commemorating the event they would not have wanted to portray the colonists as hiding and trying to get the blame pinned on others.
#3, I've refused to watch the recent AC3 footage so I don't know if the mission actually did show NPCs dressed like natives.
#4, Assassin's Creed takes place in an alternate universe that while being SIMILAR to ours, is not exactly the same. Many things in it COULD have happened in our history, but as far as we know did not. For example in AC by the year 2012 the movie industry has collapsed, and Abstergo is a company which owns majority stock in every company above a certain size, though shadow corporations and in rare cases directly. Things that are not evident in today's world of 2012.
#5, and finally, the Animus is not a perfect interpretation of events. Consider the concept of viewing the memories of someone who never did any thing their whole life but stare at a wall. In an animus session, you would only be able to do more than that if the animus was able to pinpoint the location which the person was in, and the probable architecture that surrounded them. Since the Animus creates entire cities, and no person has ever looked at every single part of any one city, it's obvious that it doesn't just rely on memory. It reconstructs environments partly through its own personal database, such as paintings, maps pictures, and whatever of that specific place at that specific time period. It's not a time machine, it's an interpretation of another time. Thus is is not infallible.
