I believe that non-violent protests should be met with non-violent force as much as possible. As far as treaties go, the Treaty of Fort Laramie was violated about 150 years ago. If we were to suddenly enforce all the treaties signed in the 1800s, there would be mass chaos. When nations violate treaties, the general idea is to move to sanctions of some kind, but obviously unless the sioux can get a major world power to back them under something like the UN Declaration on the Rights of Indigenous people, that's probably not happening.
There are other federal laws involved. It has been unclear to me personally what is in violation or not, but that's why there are courts and the Sioux have lawyers. There was clearly an abbreviated process, but I'm not sure anything would have been different otherwise. The Sioux weren't bickering about the proposed route, they wanted nothing short of the pipeline not being in their watershed. It's a long way round the Missouri river.
A UN human rights expert has made some declarations in support, however, about the use of excessive force, and I think this is the part to focus on. What do you do when people occupy private land and burn vehicles and tires? You could ignore them until they go away. That completely repudiates the rights of the property owner, but it can and has been done. Federal or municipal property, like that involved in Occupy encampments, seem a different matter.
What if I sit on your front porch in protest of your loud parties? Simple, I get taken away and charged with trespassing. If I resist, I'll get (hopefully) proportional non-lethal techniques used to subdue me. I really don't see this as much different, though I don't mean to disparage the reasons behind these protests as petty like my example.
ACLU, for instance, has talked about the excessive force of drenching protesters with water cannons. They don't make a whole lot of suggestions about the form of appropriate force. I've looked around a bit, and it is hard to find anyone who isn't suggesting either that the protesters have a right to stay there indefinitely, and those that think any force barring mowing them down with automatic weapons is a problem.
In general, I think people have a hard time separating who is right from the tactics used. One of the larger clashes involved protesters attempting to breach a police barricade. These barricades are being used, from what I can tell, as siege lines. Cutting off the camps and reservation from nearby cities, supplies and reinforcement is an aggressive and provocative act, but not violent in any traditional sense. These are common tactics used against medium to large groups and secure surrender with less bloodshed. Cut off power, water, food, reinforcements.
I don't have a great summation or conclusion. Frankly, I don't have a lot of support for either side. I think it is silly to be so distraught over one pipeline, and the irrational fear of its failure. There are far more likely things to harm a community. On the other hand, I'd like to think that police that were not so highly militarized could be less aggressive when dealing with non-violent protest and/or trespass.
