Dragonfly,
I know you are specifically looking for SA programs outside DoD/VA, but just as an aside - is this Soldier receiving treatment for PTSD? It sounds like the implication in your post is that his/her SA issues are secondary to PTSD. In the case he/she is receiving PTSD treatment, I would advise (disclaimer: I am not an expert) that he/she stay in-house of whatever program they are currently under...I'm just thinking in terms of continuity of treatment.
Obviously if this person is receiving PTSD treatment at the VA, I understand that disclosing a SA problem may not be an option. I think this presents a potential dilemma, at least from a financial perspective. If this Soldier is not on orders for treatment (and has no civilian healthcare) they will be paying out of pocket for any medical expenses. Just thinking out loud here, I'm sure you've already gone through all these scenarios.
As far as the outside SA programs, I think the best options depend on the specific substance. If this person is having an alcohol problem, AA and similar tenant programs could be helpful...but I am not sure how much this person could relate their PTSD/combat issues with other civilians who are suffering from alcoholism. In lieu of one of the forum members/moderators offering their thoughts, I would consider contacting the DAV to see if they have any thoughts/programs available.
I hope this Soldier gets the help he/she deserves and everything works out. Good luck.