Which presidential power gives the president the ability to control what happens inside departments and agencies during their terms and to shape the federal judiciary (including the supreme court) far into the future?

it was certainly a debatable decision, mainly because it was based primarily on political - and not on legal or social - views. since the congress at that time was led by members of the republican party, and the territory that the tribes wanted to turn into an exclusively indian state was predominantly democratic, the proposal (as expressed in the constitution) did not succeed, but the constitution itself proved to be of crucial importance in the creation of the state of oklahoma, and, most importantly, it guaranteed the involvement of representatives of the indian tribes in the government of the future joint state.  

as a member of congress, i would have voted to ratify the constitution, or at least to have it tabled. ignoring it was an interested and partial decision.