Throwing that flag is not going to make you many friends in the state office when that report gets filed. Don't play their game. Because no matter what you write, here is a synopsis: "I called a USC foul because they wouldn't do something I told them to do, even though there is no rule requiring them to do so other than me being a control freak."
Just tell them:
"Gentlemen, if you aren't shaking hands, I'm assuming you are trying to intimidate someone. Well, consider yourselves notified there will be nothing but sportsmanlike behavior on this field tonight, and anything else will draw flags or ejections, without any more warnings. Do you understand what I have just said? Now, would you like to shake hands with me and the other captains?"
If they still refuse, OK, they are now on a short leash, from the coach on down. It's a whole lot easier to justify a foul during play than one at the coin toss for "failure to shake hands". And if their behavior during the game is exemplary, great, then who cares if they shook hands?