officer safety doesn't trump my safety.
First, if I'm on the side of the road with red and blues flashing, chances are I am either broken down and aid is being rendered, or, I'm being "taxed" at the barrel of a gun while the local revenue generators make society safer for terrorists...
Still, they've got a job to do, and deserve no roadside contempt that they don't earn. My driving and post traffic stop behavior won't change because I have a firearm on me - stop as is convenient, light on if dark, window down if raining, both hands on the wheel until greeted. I recite the location of d/l and reg. before moving my hands. I obtain said documents and proceed.
If I produce the permit and I'm asked for the firearm, I will clarify if they are asking me for the gun, or ordering me to surrender it. If the former, I politely decline, if the latter, I ask for the patrol sergeant to be present, or offer to render myself at the speed limit to the station and agree to exit unarmed when instructed.
That said, I think this is blown waaaaaaaaayyyy out of proportion in terms of when and how this happens. Back in '96, a coworker was detained in a somewhat similar manner - This was in VA, when shall issue was but a year and change old. he was pulled over on a revenue generating stop, produced his permit and the fun began. At gunpoint, he was ordered out, hands on car, physically disarmed by the officer, unloaded gun put on the hood. This went on for about 15 minutes until another cruiser arrived. He got a warning, the officer got a complaint filed against him and my coworker eventually got a letter of apology from the traffic patrol commander. Once the police are more accustomed to seeing the armed people, I think they also get a little better at "reading" people for when they're going to be a problem. I think your demeanor probably has a lot to do with it once the police are accustomed to the new way.
In Virginia, we're only allowed open carry in alcohol serving restaurants, and I routinely do so, often running into Fairfax officers. I've never gotten any snide comments, disapproving behavior, undue attention or even a bad vibe. One officer kept an eye on me and my friends, but nothing out of the ordinary considering the 12 or so open carrying patrons...
I think another poster suggested contacting the local law, and I second that. Ask to talk to the patrol division, and ask directly what they want to see in the way of conduct etc... Once it's been on the books, cops will learn the good guys and know they're not a threat.