To remove the remains from a museum to their resting place. To what purpose? So that the remains may "rest in peace"? Doesn't this imply a supernatural -- even religious -- connotation? But...but...if that's the case, and seeing NAGPRA is a federal mandate, what about the separation of church and state?
I personally, am not against NAGPRA, at least in many circumstances (some of its wilder applications are a little bit questionable). The collection of native cultural material and remains around the turn of the century was unethical to say the least, and NAGPRA is a positive step for native relations. If the graves of my great grandparents were dug up shortly after they were interred so that they could be put on display as savages, I would probably be pretty upset too.
On the other hand, in extreme cases NAGPRA can be quite questionable. Probably the most prominent case is that of the Kennewick man, which I'm sure you could find plenty of documentation on, if you are interested.
And, in my humble opinion, even if there is a "seperation of church and state," the state should be allowed to protect the inviobility of human remains at the request of the family/ancestors.