By the time that it happened, I would say that the massacre was an exception to American policy towards Native Americans. It was much more in keeping with the way things had been decades before at, for example, the time of the Sand Creek Massacre.
By 1890, US policy towards Native Americans had turned much more towards trying to assimilate them into US society. 1890 was, after all, three years after the passage of the Dawes Severalty Act. This law was passed to promote private land ownership among the Native Americans. The Carlisle Indian Industrial School had already been in operation for more than ten years. The creation of boarding schools and the passage of the Dawes Act show that the American policy was now that of trying to "kill the Indian to save the man." American policy was no longer centered around literally killing the Indians. It was much more about trying to make them like whites.
Therefore, the Wounded Knee massacre was an exception to the policy that was current at the time of the massacre.