I live in Dutchess County. My wife had a hard time getting her permit because she had been diagnosed with post traumatic stress disorder after her mother and sister were murdered by her step father (sixteen years ago!). She had to get a note from a psychiatrist stating that there was no contra-indication for her to have a firearm. It took quite a while (and a pretty penny) to find a doc who would see her for permit purposes. Most of them simply said "we don't do pistol permit evaluations."
They knew about the diagnosis because we put it right on the application. We wanted to be completely forthcoming and honest. Better to have them deny it at the start and fight for it, then to have them deny the permit for "lying" on the application (even though we didn't think it really applied to the purpose of the question). Then we would have no recourse. She does have her permit now, and we're getting ready to go get her first handgun soon. Woo hoo!
Anyway, sorry to go on about my experience. In your case I would say have all your paperwork in order when you see the judge. The doctor's professional opinion is that you are not a dangerous person to carry a firearm. If the judge says otherwise, you have great grounds to sue. The judge is not qualified to evaluate your mental health, only a doctor is. By that time the Supreme Court most likely will already have ruled that the 2nd is an individual right (DC vs Heller). I think you would have grounds to say that the Rockland judge is arbitrarily imposing unreasonable restrictions on your individual right to keep and bear arms. If you lose your civilian permit, your c/o credentials should still allow you to carry with your badge. This should give you time to fight the Rockland judge.
If you do get your permit pulled by this brady-on-a-bench, I think some of the pro-gun organizations out there might support you in an effort to use your case as one of the first to push forward after the new Supreme Court ruling. Such a case would make other judges think twice before imposing their own values on others' rights.
DO keep us informed as to what happens when you meet with the judge! We are all keenly interested.