Uncle Sam Grants Permission to Native American Tribe to Kill Two Eagles

The U.S. Fish and Wildlife Service has granted a Native American tribe a permit to kill two bald eagles for religious purposes. Last year, the Wyoming-based Northern Arapaho tribe filed a federal lawsuit because it believes that when the government refuses to issue such permits, it is infringing on the tribe’s right to practice its religion. 

For the record, and according to an Associated Press article by Ben Neary, Native Americans presently receive eagle feathers and carcasses from a federal repository based in Colorado. It is illegal to possess eagle feathers or carcasses, unless you have a permit.

Bald eagles became an endangered species in 1967.The Interior Department removed the bald eagle from the Endangered Species List in 2007, but it is still protected by the Migratory Bird Treaty Act and The Bald and Golden Eagle Protection Act.  The Eagle Act, passed in 1940, does not allow for  "take; possession; sale; purchase; barter; offer to sell, purchase, or barter; transport, export or import, of any bald or golden eagle, alive or dead, including any part, nest, or egg, unless allowed by permit." In order to apply for an eagle, which might be delivered on ice from the repository, a person must present a Certificate of Degree of Indian blood and also belong to a federally recognized tribe. 

I wonder about the separation of church and state here. Is it proper for the government to mandate whether Native Americans can practice their religion in accordance with time-honored traditions? Is the North American Wildlife Conservation Model applicable to reservations, since those are technically sovereign nations?