You did the right thing. Fighting with him would have only made it worse. Going through a stop sign, he can claim a reason to ask if you have been drinking or under the influence. Right or wrong, in a court nothing he did could be seen as some sort of wrongdoing. Even if he was just being a jerk, he has his bases covered in this case. Since you ran a stop sign, he can claim it might have been because you were impaired by something, even if you were not.
I remember years ago I was pulled over (en drab) because I passed a cop with my high beams on. The first thing he asked was "Have you been drinking?" He said he though the reason I blinded him with my high beams was because I was impaired (I wasn't, I was tired and just forgot to do it in time.) Sure, I could have complained about being asked if I had been drinking, but it would have fallen on deaf ears anyway.
