Well, having done archaeology on FN land, doing anything on their land without express written permission before hand is not only illegal but dangerous. You could easily become part of the archaeological record that way. In some cases, however, permission can be arranged but will usually require reaching agreements on disposal of any and all material recovered prior to commencement of work. If you don't like the conditions established ahead of time, you just don't work there.
As to human remains elsewhere, in both the US and Canada there are both ethical standards and laws against disturbing human remains no matter where they are found. Simply, digging up an unmarked prehistoric burial is no different from digging out burials from an active cemetary, no matter what your reasoning behind it. To me, there is no real difference between digging up burials to get the pots or arrow heads and digging up burials to get the silver fillings and wedding rings in them.
Still, burials do come up in development projects or erode out from natural processes. The former is sometimes dealt with in CRM (more in Canada than in the US - the latter usually only occurs on some federal projects while Canada seems to offer more protection on housing projects, etc. but not always and not often enforced or policed.
Kennewick, however, was a case of the latter. The remains were found eroding out on Federal land and reported to a local archaeologist. The controversy began after this point.