I think clean slate would be the only fair way to handle it, for two reasons:
1. Since the new system is binary, there isn't really a way to outright put someone on "thin ice".
2. The point of these kinds of systems in the first place, especially a zero tolerance one, is for people to change their behavior and not act like that in the community. I would rather not permanently cut people from all IHLs unless absolutely necessary. I believe people can change, and that they can learn from being removed from the league due to flaming. There may be some people still that will consistently do it and get removed from IHL after IHL, and those can be dealt with on a case by case basis.
Kicking the player.
The way I see it, the choices there are either kick the player, still giving the rest of their team a chance, or penalizing the team a match, potentially causing them to be eliminated from the league. They they would be flamed AND lose a game because of that player, which is not really fair.