Users set themselves up for this shit by insisting on hot wallets.
Be willing to have the admins run their monthend trial balance until it balances before doing their monthly accounts-payable payouts and maybe there would be less of it, though even then arguably hackers could hack carefully enough to ensure the trial balance balances so that the admin will likely go ahead and run the payouts even though the wrong people get paid.
Another way to work around it is sheer volume of users combined with high enough fees, so that even if a hot wallet is emptied totally the loss can be absorbed by the site (admittedly due to having been passed on to the users in advance in the form and size of the fees).
-MarkM-
I would rather a pool that just pays what you are owed every day. No need for any manual or limit trigger withdrawals - an admin should look over the payments each day to make sure nothing is fucked up.
Of course, a CPPSRB pool should never have had this problem. The fact this happened shortly after the un-warned move to PPS and back to CPPSRB when people complained strongly points to fraud. A properly configured CPPSRB system should never be able to inflate balances beyond what is payable (49.5LTC/block found). If the admin's story is true, the false earnings should have gone into shelved balances, not payable balances.