Wouldn't have much input
I got off of active duty in the JAG Corps this summer. My first thought is that while I may be asked my input as to whether you were an otherwise good soldier, the HHC Commander is going to be the first decisionmaker in the process (unless there is an appicable witholding policy in place). The JAG will not have much say in most cases. If you worked in crim law shop or were a brigade paralegal, they will probably get another office to handle the case/offer advice to avoid appearance of impropriety.That being said, it will be proceessed like any other case most likely. Depending on the command, most likely an Art. 15 and a Chapter (unless you want to stay in, in which case just the Art. 15).
The only thing that may happen is bc of your job, if you were otherwise great, and had a compelling explanation for your AWOL, they may make everything locally filed. Otherwise, I can't see you having a future career. Many facts will impact your case like your grade, succesful deployments, other disciplinary history, etc.