Okay, I'll rant.
The episode was loosely based on something that actually happened up in Washington State about 10 years ago, involving the discovery of really really old remains-9-10,000 years old. The archaeologist who first examined them thought they looked Caucasian, which started a huge pile of trouble. You can find that story here.
At any rate, the issue in the episode was that ancient remains were found on private land and the tribe was worried that the age of the remains would negate their claims to the land they owned and the casino they were running.
Problems with that:
-- State law controls human remains found on private land, so the state should have been involved. The federal government has no involvement on remains found on private land unless they somehow end up in a federal collection.
-- The remains were worthless scientifically without proper documentation of the site, which is what you need to publish your results. Stealing the skull from the site made it useless as a piece of evidence: any archaeologist would know that. There would be no point in stealing it. (Also, I like Reed Diamond, but he made a piss-poor archaeologist--far too clean-cut and preppie looking.)
-- The big problem is that the episode got the law about the tribe's concerns backwards. The tribes' reservations are recognized by Congress and the Indian Claims Commission, which ruled in the 1960s and 70s based on historical and ethnographic data, recognizing traditional land claims. There is no legal reason at all why the tribe would fear losing their reservation because of the age of the bones. Now, the tribe might be upset that scientific evidence might indicate that their religious beliefs were wrong, that they weren't in fact in the area from the beginning of time (although he could have been a traveler, after all), but they had no reason to feel threatened in the way the episode described.
-- Oh, and then there was the part where the lawyer refused to tell them any other archaeological sites because then people would raid them. Federal law strictly prohibits revealing the location of sites to anyone who isn't an archaeologist working for the federal government on a project requiring that information. Which the tribes know very well. Also, it's one thing to give a general location, it's another entirely to find a site based on that.
Argh! They shoulda called me, I would have saved them this embarrassment. So many wrong things.