Not to get technical, but..... you virtually admitted to breaking the law after he asked you if you knew why he pulled you over. The game was up IMO at that point. You had no "right" not to comply. But, you handled it like a champ, and he probably gave you a break because you made an admission of guilt right from the beginning. What cop doesn't like bikes and guns anyway?
Its not like I admitted to robbing a bank or somethin...I knew why I was pulled over and I had no reason to lie. It obviously helped my situation dont you think?
There is one tiny, tiny, tiny little thing. If you let him disarm you and he accidentally (esp with Glocks) puts one in your leg......
I thought of that, believe me...but It was a risk I was willing to take to ensure the Officer felt safe with me. After turning around and seeing the SWAT lapel pin, I knew he was familiar with Glocks...

Maybe an appropriate response also would have been "Officer, I want to cooperate and I'm not a threat to you but I don't feel comfortable having you remove a gun from my person. If its ok with you I will slowly unholster it and close it up in my saddlebag until our business is complete". Not sure if this would work every time, but I think it would be the best response.