The 'monument' to Johnson near the end

I always thought it was sort of a tribute to JJ. This does not mean that they still don’t want to kill him. They just honor him due to him being a courageous and deadly rival. Sort of like the beginning of Last of the Mohicans; they honor the deer but they still kill it. I think this is reflected in the discussion with the settler he comes upon. Clearly, the settler sees JJ as a legend. This is the way I saw it although there could be more to it.

Having failed to kill Johnson, the Crow are now engaging in what could be regarded as magic; in building the shrine they are simultaneously acknowledging Johnson as their mightiest enemy and honouring him for his prowess, while seeking, through divine petition, to protect themselves from further harm at his hands. The concept of 'powerful medicine' is at work here also, in the recognition of Johnson as a fierce, brave, and honourable enemy. The repeated acts of 'offerings' serve to keep the shrine 'fully charged', as well as to ensure safe passage through what has become, for the Crow at least, dangerous territory.