I don't get it. Slaves freed under the Emancipation Proclamation became citizens of the US-- the nation in which they resided (were owned). If they resided in the Cherokee Nation (were owned there), how is it that it could be justified not to include them as part of that Nation...

Well, here is a mini timeline:

       "Trail Of Tears" relocation: 1838-1839

       Emancipation proclamation: 1 JAN 1863

       Oklahoma (the part of Indian Territory where Cherokee were relocated) becomes state: 16 NOV 1907

The point of moving the Indians was to provide lands for a self-sufficient nation outside the United States rather then inside the United States.