Let's see if I am following you.
You have an as of yet un-named medical condition.
This condition prevents you from participating in PT.
You have gained weight due to the fact that you can not exercize.
Your command is aware of the medical condition, but is proceeding with the steps to chapter you out because you have gained (too much) weight.
How long have you been in (what branch too)? How long have you been complaining of the sysmptoms, and what Dr's have you seen so far?
I suggest that you request to see the Rhuematologist ASAP. Explain to him that you beleive you have AS or one of the related diseses. The joint pain, eye inflamation (Maybe Iritis) and the fact that you have the HLA-B27 marker points towards AS. It can take years to get a DX for this disease. It is extremely important that they figure out what you have prior to be discharged for any other reason!
Sending you to the Rhuem for the eye tells me that at least on DR was thinking AS...
AS/PsA DX in 1988
Retired on disability
in 2005 at age 44