Ok, about that.
A Law enforcement office can and MAY detain you once a weapon is found, until it is determined that you pose no threat and are not being arrested. Being placed in handcuffs is not a violation of your civil rights. Cop saw a gun (probally unannounced), did what he determined to be the correct course of action until which time he found that the gun was 1. unloaded and 2. not stolen.
Sounds like your buddy needs to get over it, and learn to either put the thing in the trunk (not required but still a good idea), or learn to speak up to the officer and let them know "I have a firearm in the car, it's UNLOADED but I do have one (the whole time keeping hand on steering wheel until told to do other wize), what do you want me to do?"
People don't understand that a LE's only desire is to go home to loved ones at the end of their shift, and they do have one of the most dangerour jobs around, so yes they can be on edge.