My interpretation of the story and its ending
Probably not stuff that hasn't already been said somewhere in some form or another, but I thought I'd share my thoughts anyway...
I saw the story as a spiritual journey. Life is hard and humans are always looking for guidance, hoping that some signs can lead them to green pastures. In Meek, the group at first has a white American type leader. He's quickly revealed to be winging it, making things up as he goes along, never admitting that he's as lost as his fellow (life) travellers. Once we're done with the false prophet, the next stage of the movie introduces two new possibilities: female leadership, and a native's guidance. This is how the film becomes a revisionist Western.
Michelle Williams' leasership offers resolve to go on, as well as kindness towards the people of the land. It's a contrast to the white man's arrogance who claims he knows best, who will brush aside the people who are actually living in the land, and who will in fact convince himself and his followers that they are evil and ignorant.
What the Indian offers is a more mystical, more natural kind of guidance. By following him, what Emily is essentially doing is she decides to stop trusting the lies of self-appointed leaders and to listen to the signs of the land itself and its people, who offer strange and otherworldly signs. She takes a leap of faith into the mysterious. Will that lead them to the promised land? As in any religion, there is always a component of doubt. Certainty is ever out of reach, always beyond the next hill. But there are signs along the way. That's what the tree represents. It's a sign of hope, and the movie closes on that hopeful note. I think this is more interesting than the fact of a succesful or failed journey would have been.