We've corresponded with the author of the article, who provided a link or two, plus some digging of our own. This bill (or the section involving the change to NAGPRA) was apparently sponsored by former Sen. Ben Nighthorse Campbell before leaving office. See here for the references to the bill, specifically:
Amends the Native American Graves Protection and Repatriation Act with respect to the definition of Native American.
SAA's (SOciety for American Archaeology) position seems to be that they are/were against this for procedural reasons. See here (5 Oct 2004):
Because NAGPRA is a compromise law formulated
through an open, deliberative process
involving all the concerned parties, SAA is
opposed to changes in this important
legislation being made without a full and
open hearing. SAA is not opposed to the
substance of this proposed amendment, which
affirms the Society's position that the
definition of "Native American" was intended
to include tribes, peoples, and cultures
that were once indigenous to the United
States as well as those presently recognized
as indigenous, but we are strongly opposed
to the process through which this amendment
is being put forward.
We are unsure as to how this squares with SAA's previous arguments regarding Kennewick and court decisions associated with it. For example, on 3 Sep 2002, SAA generally agreed with Judge Jelderk's decision that, in cases where cultural affiliation to any existing tribe cannot be maintained (generally, we assume, due to great age), repatriation cannot be implemented.
On further review, however, it seems SAA is more concerned with the portion of the decision (and the plaintiff's -- i.e., the scientists' -- case) that designates the Kennewick remains in particular as "non-Native American":
. . .SAA disagrees with a key element of the plaintiffs' argument: that Kennewick Man was not Native American according to NAGPRA. SAA believes strongly that the remains are indeed Native American, which is defined in the law as "of, or relating to, a tribe, people, or culture that is indigenous to the United States."
(From FAQs on the SAA's Amicus Curiae Brief in the Kennewick Case, June 2001)
Also see here for the SAA's distinction:
Although SAA agrees that Kennewick Man is Native American, we believe that the Secretary's decision on cultural affiliation is fundamentally flawed in its understanding of the term "cultural affiliation" and in its assessment of the evidence presented for cultural affiliation.
Hence, it seems that the SAA at least is comfortable applying the term "Native American" to any set of remains found that date to pre-contact times, but that in order for repatriation to occur, cultural affiliation must be demonstrated.
We are unclear as to how this new implementation will change things. It appears as if the previous rulings regarding Kennewick -- that he is not "Native American" -- preclude NAGPRA from coming into effect in the first place, even before any sort of "cultural affiliation" can be demonstrated. That is, if it's old enough, NAGPRA doesn't apply, and nothing happens. Defining anything pre-Columbian as "Native American" would automatically bring NAGPRA into account, and force any parties interested in repatriation to demonstrate cultural affiliation.
So, it may not have precisely the far-reaching consequences we thought.