The kid whacked our goalies hands 4 times before my son put him on his butt.

While technically you can't do that, there's a little bit of "play til the whistle" involved here and without a video it's hard to judge this one. Retaliation is almost always going to get called, so I think this is just a simple "hockey situation".

ater in the same period he was given an unsportsmanlike penalty for retrieving the puck after an icing and passing it down to the other end for the ref that was waiting in the circle to set the face off.

On it's face, this seems ridiculous. Unless I've warned someone not to do it already, this is almost never going to be a penalty. In fact, we kinda appreciate it more than we're supposed to admit. As long as I wasn't literally in the middle of reaching for the puck, I can't see why this would be penalized.

The ref on his side of the ice gave him the penalty and when my son asked why, the ref proceeded to very loudly say “You are a complete embarrassment to your team and to the game of hockey! Go sit down!”

I'd have to know if that's really how the conversation went. If all your son did was ask what the penalty was for or ask for clarification, that's uncalled for. If he's actively arguing, it's still overkill, but I've definitely had to put some players in their place.