oh yeah, especially and particularly with a stallion. They need immediate response, and if they insist on upping the ante, you must rise to their occasion. Respect is all of it. A whack across the ears with a crop handle is not likely to be hurting him much, but it will definitely make him think about not doing it again - though it sounds like in this case, he's come to the trainer to solve an already ingrained problem. Those who have not had to deal with a rearing horse don't get an opinion, in my book, on handling it.
Sidereins on the hotwalker..... that's interesting. I'd ask first why the sidereins? Does he try to chew or tear down the walker lead? or does he try to flip over and do other stuff that the sidereins don't let him do? Multiple possible issues on this horse, from the OP's description.
I would definitely do another visit when the BNT is back - and gently ask HIM (or HER) if the young stud you saw on your first visit is coming around, as he's SUCH a good-looking horse. See what the story is and have more info to make a decision - all "assistant trainers" (or working students or whatever) are not created equal.