Illegal occupation,?, so any protest, as this was, should be illegal? They had arms, but they did not use them or threaten anyone. They were protesting the unjust jailing of the Hammonds. If vandalism is the measure, there should be a lot of folks in jail who protested the pipeline. This is also about the inappropriate taking of public lands, and there seem to be some financial interests driving the FBI reaction to that.
They brandished arms, by some accounts made threats, and they encouraged others to arm themselves and join them. That is way, way beyond civil disobedience or protest. This was no peaceful sit in. They were armed.