Ralph:
If you had a problem, I contend it was because it either wasn't being coached or officiated properly before. As I said earlier, in 17 seasons, I have seen ONE instance of a player trying to take a cheap shot on a kneel down play, and that was in a JV game. I NEVER saw it happen in a Varsity game, not once. In that JV game, the player was ejected, and his own teammates literally grabbed him and pulled him off the field.
It's a non-issue, and I don't like officials injecting themselves into plays in this manner. We already have rules for these situations. In your scenario, why even bother going through the formality of kneeling? Coach A says we're taking a knee, Coach B says we won't rush - OK, the game is over. The coaches have mutually agreed to end the game early, again, something that is allowed by rule.
Going through the 9 points or less, check with each sideline, agree not to rush or play - needless waste of time. And if a kid is bound and determined to be a hothead and blast a kneeling QB with a cheap shot, this rule isn't going to stop it, in fact, it might make it easier because the offensive line will relax based on the "agreement".
Want to really discourage these actions? Make mandatory suspensions for players that are ejected, the ejection is doubled if it's in the last minute of play. We have the mandatory suspension part now ( but not the doubling in the last minute), and if you are a senior and you can't serve your suspension in football, it carries over to the next sport you play. So now you are sitting out the first two basketball or baseball games. The only players with "nothing to lose" are seniors in their last game that play no other sports. That's a small enough percentage that we can deal with those.
Again, if this is a problem in Maine, just end the game. That's the only real way to stop it.