I think the most calculated way to go about this would be to write a note while in your car that says "I will do as requested as long as no guns are pointed at me.", stick the note out the window, and close the window on it if you don't have tape, or find some other way to affix it there because you want your hands on the wheel and visible so they know you are not a threat worthy of threatening with death by pointing a gun at you.
If a note on the window seems too "suspicious" to "security" minded individuals like cops, then saying those words might suffice, but they might not give you a chance to speak between the yelling and the gun pointing. Of course, to use a note on the window you would have to already see them drawing people out of their cars at gunpoint, so chances are in most situations you would start out seeing them pointing a gun at you, at which point you would have to say the phrase.
Even then, would they understand? Would they back down, lower their weapon, get the information they need from you (that you are innocent) without pointing a weapon at you and without searching your car (or get a warrant), and move on?
Or would they escalate the situation, continue pointing guns at you, break into your car, hurt you, imprison you, or possibly give the death sentence on the spot for passive, non-violent resistance which was only demanding to be treated like a human being instead of a slave, and while making it clear you would do as they asked (within the boundaries of the law -- they still need a warrant) so long as they treated you with respect?
I don't have the answer, but this question would be rather important to me if I get pulled over and they point a gun at me.
I would try to make it clear that I am not "resisting". I would try to be polite, and would be sure to mention first that I will do as asked before mentioning that I won't unless they lower their weapon, because if they first thing they see or hear is "lower your weapon" they would be on-guard for danger.
I would not be armed, I would not make any threats, I would not harm anyone, but I would do my best to make sure they do not violate my liberty by pointing a gun in my face (a sure violation of my right to life) or searching without a warrant.
This would involve talking to the cops to a degree, which I am aware is ill-advisable. But you have to use some words to refuse consent to a search, too. I would otherwise remain silent, even knowing I am innocent, as it is my right to do.
And I wonder what horrors would be in store as a result of that peaceful, non-violent, legal act. The outcome may depend on the cop and the situation, but we are assuming a situation in which they feel it necessary to be pointing a gun at you (and made this decision without even knowing if you were dangerous or anything else) in the first place.
Demanding even a "good cop" to lower their weapon before you do as they ask might be not only infuriating (it might be to the average person, too), but they might consider it against security policy or something.
But I
demand not to be treated like a slave, and I don't care if that makes them feel uncomfortable.
Does this look like how you would treat an innocent citizen, or a slave that gets tossed around until you feel like tossing around the next one?
I probably would say things to cops, though. Things like "Please don't kill me. Please don't kill me. Please don't kill me." until they get the point that pointing a gun at someone is traumatic.
I expect them to create a doo-hickey that allows cops to create their own warrant instantly any day now(just to keep up appearances)... 
