If a home team has a substantial pitch invasion, penalise the team.
Put some responsibility for the club on the fans. You can call it failure to provide adequate crowd control.
League - 30 point deduction (realistically enough to destroy your season regardless of where you are, can always apply it for the season after if a team is confirmed relegated)
Cup - Automatic forfeit of the next round (if you're losing, the team you draw next year goes through without playing the game)
It's just gone too far now. I get the excitement but it's our 6th PL now and breaking the crossbar was too far. Act like you've been here before. The Billy Sharp and Patrick Vieira incidents are even worse.
I get its over the top but to me that's how you shut it down. No fan wants to be the reason their club gets relegated or loses the title.