Part of this is the result of the "Peace Policy" adopted under President Grant. Now the actual "Peace Policy" as implemented by Grant was actually an improvement, by the 1880s (When Grant was long out of office, his Last day as President was March 3, 1877) the policy of "assimilation" was adopted and part of this was the "Americanization" of Native Americans. This was pushed by General Platt who founded Carlisle Indian School in 1879. Here is his part of his 1892 report on this policy:
Indian schools are just as well calculated to keep the Indians intact as Indians as Catholic schools are to keep the Catholics intact. Under our principles we have established the public school system, where people of all races may become unified in every way, and loyal to the government; but we do not gather the people of one nation into schools by themselves, and the people of another nation into schools by themselves, but we invite the youth of all peoples into all schools. We shall not succeed in Americanizing the Indian unless we take him in in exactly the same way. I do not care if abundant schools on the plan of Carlisle are established. If the principle we have always had at Carlisle—of sending them out into families and into the public schools—were left out, the result would be the same, even though such schools were established, as Carlisle is, in the centre of an intelligent and industrious population, and though such schools were, as Carlisle always has been, filled with students from many tribes. Purely Indian schools say to the Indians: “You are Indians, and must remain Indians. You are not of the nation, and cannot become of the nation. We do not want you to become of the nation.”
http://historymatters.gmu.edu/d/4929/Thus, the policy of the US till recently (1960s) has been forced assimilation. The Churches were both part of that policy a victim of that policy. To make a Native American a "Christian" was one of the ways to make Native Americans more of an "American". At the same time the same policy required those churches to look after their members NOT as Native Americans but as "White Americans". The later made the Churches victims, for it undermined whatever support among Native Americans the Churches had AND also meant such Churches could NOT be used as Churches have been used for in the past, as rally points for grievances of its members.
People tend to forget that since people meet at churches, they talk to each other before and after mass. Thus Churches are traditional places to meet and form groups. Early Unions tended to be Church Related, not because they members were one religion or another, but it was a place where many potential union members meet and could meet and form groups.
One Historian called the American Revolution the "Presbyterian" Revolution, for it was the Presbyterians who ended up being the back bone of the Revolution. Congress and the States ended up sending their messages to the people via the Presbyterian Churches who tend spread them to other churches who wanted to get the news. The American Revolution was NOT a religious war, but religion was how the sides formed up. Presbyterians, Congregationalists and other "Reform" Churches supported the Revolution. Anglicans (Church of England, Episcopalians) supported the Crown (Catholics, Lutherans tended to support who ever of the above was in the majority, which tended to be the Presbyterians in areas which had high Catholic and Lutheran populations). Thus you went to the local church to find out what people where talking about.
Now, since the invention of the Modern Newspaper (about 1850, it took the invention of pulp paper, invented 1801, and steam ships and railroad to spread those newspapers) Churches are NO longer the places you go to get the news. Radio came into play in the 1920s, Televisions in the 1950s when it comes to news.
On the other hand, Churches are still a place for people to meet and discuss things. You be surprised at what was founded (and had their first meeting) in some church's basement. IT is this function that the Churches on the Reservation have failed to provide. Such Churches are depended either on the Government or outside donation that they do NOT want to risk being the location of radicals, even if such radicals are their own members (and even if the Parish Minister or Priest supports the Radicals).
Thus I believe your statement of lack of support of, for and by the Churches of the reservations. It is a product of the past 140 years policy of force assimilation.
= new reply since forum marked as read
