First and foremost I want to tell you that even if your son is chaptered, he still has care and compensation available from the veterans administration.
A general discharge will entitle him to most benefits
He will loose the GI Bill...but retains the ability to seek treatment and compensation (money) from the VA. It sounds like he will need both
Now, on to your question...what can you do now?
I would have submitted a letter from a doctor that links his PTSD to this misconduct.
That would be highly relevant
If today is the deadline? It may be too late. But that is one thing that could link the misconduct to the disability
I agee that the Army regulation that applies gives policy guidance that tells commanders that they should attempt to rehabilitate...and linking the PTSD, to the actions, through a mental health professional can help you argue that for policy reasons he should be retained.
Just understand that the separation authority has discretion...so they can decide needs of the unit require separation in this case...so it is all about convincing the separation authority to not separate.
If you can get a letter from his doctor, in the near future, I would have your lawyer or your son submit it. It can not hurt and may help.
Other than that? If today is the deadline for submission your options are limited. I agree...it sounds like your lawyer did a poor job....you can consider a malpractice claim against them.
And your son should file a claim with the VA...regardless of how he separates he needs to do this...sooner is better.
Please let me know if you have more questions