I agree that the stop sign was probably because I was the assistant and it probably didn't help that the HC was already sitting on a T from earlier, but as I've said before coaches are people just like officials. Talk to the assistant coach in this case or as I said in the OP tell the HC you don't want to hear from the AC, but the stop sign is childish.
That being said...when I'm officiating I don't mind responding (especially in this case during, a dead ball, in close proximity, not yelling) to an assistant's respectful question or request.
BTW...HC in this case after the game said to me that he enjoyed coaching from his seat and he might try it the rest of the season
