Rachel, when you have a resident causing property damage, you should follow your protocol for addressing the issue. I would certainly give them a Quit or Cure based on the property damage alone, domestic disputes causing problems for neighbors and having the unauthorized pet. I would also issue work orders to repair the damage (at least to the door) and charge them for the replacement/repair costs.
It is quite possible the returning Service Member has some issues with reintegration but you are not a physician equipped to make any such diagnosis, so until he asks for special accommodations for a disability you have no reason to treat this family any differently from any other resident family.
Once someone from Military Housing contacted you, then your resident waived any right to privacy regarding the issues the Military Housing Officer brought up, in my opinion. I was always under the impression from working with my military families, that I could contact my Service Member's commanding officer if there were any problems. I never had to do so because I never had any problems. I think I would keep whatever conversation I might have with the Military Housing Officer who has intervened on the resident's behalf to strictly the facts and make sure my personal opinion was never stated.
Whenever a third party gets involved, it is often at the expense of the property. Oftentimes that third party only has heard ONE SIDE. If you want to cut your losses now, you could let them out of their lease and turn over all damage charges to a Collection Agency at the proper time. That will follow them for a long, long time, especially owing another apartment community.