First, my immediate thought when I read this description was that if I were the trooper I would have questioned this guy as well. It's a sad fact that ambushes against LEO are more and more frequent. You are working a hot scene and someone accross the street is taping you and, upon further investigation, wearing a gun? Yeah, you are going to get questioned. It's a safety issue.
I agree with a lot of what you had to say. I think the only thing you wrote that concerns me is what I quoted above.
Now perhaps it's my own naivete, but why would a man obeying the law concern you and become an officer safety issue? I mean, I can sort of see your point that maybe it's possible this guy is going to ambush the police, but at what point is the line crossed by citizen or leo regarding the Rights of the Citizen and the Safety of a Leo? Shouldn't a person's 2ndA & 4thA Rights be secure even in this situation (this of course assumes the OP's account is accurate)?