You would know the layout of Ft Gibson much better than me but... I think the orientation of the photo is correct. I think the photo is taken looking east and that the landing on the west side was upstream from the landing on the east side. Malcomb & Abert's map of the Arkansas River (1870) seems to show the Ft Gibson landing a little downstream. The Adair/Bushyhead house was near the river and the other structures of the old fort and the town of Keetoowah (later Ft Gibson) would be ESE and SE from there. As I know you know, when the fort was decommissioned in the late 1850s, it became the property of the Cherokee Nation and the various structures were purchased by private individuals. So I believe the other structures in the distance are on the road east from the old stockade.
I would expect that the higher ground, i.e. where the stone barracks, commissary, etc., are would be visible in the distance but perhaps that has completely faded with age. Also, the somewhat primitive lens may have not registered on the glass negative the 'out of focus' distant scenery.
You may be familiar with the memoirs of John Martin Adair in the Indian-Pioneer Papers. See: http://goodoowah.50megs.com/indpio/%20John_Adair.htm
I thought I had seen a close up of this house somewhere online (maybe in the Chronicles of OK) but was unable to find it.