If the bones were clearly linked to the tribe, few people would object to handing the bones over; the problem is, the Kumeyaay tribe's claims are based on Native American creation myths. In reality, a Native American who lived 10,000 years ago cannot be associated with any particular tribe, anymore than the artists of the Lascaux caves can be considered French. The bones in California could be from a population ancestral to most Native Americans, or ancestral to none of them.
Obama's Interior Department is now considering whether to ignore the scientific review committee that is normally part of the decision to hand over Native American bones. As one anthropologist in the Nature news story said, this issue is going to put the Obama administration's claim to science-based decision making to the test.