It sounds to me like Kos was just being a sensible dog- poor baby had been hurt/frightened once; he'll probably get over it, but not immediately, anymore than you would recovering quickly from a mugging! Holly once got jumped on by a border collie in the park (dog hated little dogs) and although she wasn't hurt- a miracle in itself as the dog had just literally thrown a little JRT in the air, and then jumped on Holly's back and went for her neck/throat- it was a while before she became her usual merry self around larger dogs. Holly wasn't a puppy; this happened within the past year, so she was 2 at least. I'd agree with the others; find another trainer. Could you talk to others in the class? How do they feel about how you/Kos were treated by the trainer?
I'm also interested in the responses re discouraging fear. Holly tolerates the new puppy very well, but she prefers to stay out of it's way and she has that white-eyed "What the heck is going on?" look. I've been thinking that perhaps the way to get her used to the pup quickly is to control exposure to the pup, ignore Holly's nervousness, and praise her to the skies when she shows interest or lies beside me when I have pup on lap...similar sort of idea, I think,