In fairness, I think this is a slightly different issue.  "Creationism" is only being held up to criticism because of its attempt to jump the religious boundary into science.  Beyond that, no one ever went out of their way to criticize a creationist belief as held by any number of Christians.

Similarly, the Native American claim is not being elevated beyond their belief, so it doesn't enter into the realm of criticism any more than any other religious belief does.

The problem here is not scientific, but political.  It is no different than having a "holy land" in the Middle East, or a sacred place in the Black Hills.  Scientific validation has nothing to do with this claim, but rather it is going to be viewed in terms of recognizing a people's culture.  From a scientific perspective, ALL of these claims may be "full of it", but there is no compelling reason for going in and tearing up people's cultures over it. 

It also comes down to the point that few people would argue that scientists should have the right to dig up anyone they find "interesting".  Clearly our parents, and grandparents are essentially protected from such an effort, and if we look at historical figures, it is equally unlikely that anyone would think it a good idea to dig up Washington or Ben Franklin and store their bones in a museum.  Therefore, the idea that graves are to be left alone is not an unusual or foreign concept, so the only question that remains, is (1) how much time has to lapse before we no longer consider a "group" connection to anyone living, or (2) how much evidence is necessary to establish a link to a discovered set of bones.

Since most people don't have a comprehensive family tree, a few generations separation is often all one needs before there is essentially no connection.  However, in the case of tribal traditions, the problem is a bit more complicated, because even though there may not be any individual connection, the connection is viewed from the cultural perspective and, in effect, represents part of the identity of the group (or tribe).

Interestingly enough I don't have much of an opinion one way or the other on this, but it seems that the scientists should also have to advance a compelling argument as to why these bones are important from a research perspective.  It would be a shame if the only argument that is advanced is simply to have an interesting display at a musuem.