I agree that there is a lot of "insert colour here"washing that goes on, but from a macro level, there is no disputing the horrendous amount of intentional (and unintentional) harm that was done to the Indigenous population of  what is now North America.  
One need not be innocent in order to be a victim.
That being said, genocide is, in my opinion, a wrongly used term.  Culturalcide, for sure, but not genocide.  This isn't to say that the end result isn't almost exactly the same, but the motive was different.  Most of the deaths of Indigenous populations came as a result of a lack of disease resistance, not war, or murder.