I'm certainly no expert, but why not a suspended fine (the size of which is entirely dependent on how much you've overspent) pending your next set of accounts. If you're not getting your house in order by the next set of accounts (maybe the 'allowed' losses the following year is agreed upon between club and Premier League) then the fine hits. A further, larger fine is threatened for the following year, again, pending sorting your finances out.
I would also argue that any fine paid should be deductible from your next set of accounts to prevent entering an endless cycle. That way, it's the owner(s) who are being punished for their poor handling of the club, rather than the fans/staff of the club.