Yea, that particular edge case makes it pretty hard to track payments and map the transactions to database records 
If you expect a one-to-one relationship between transactions and bitcoin addresses, then yes, a multisend will be a problem for you.
If I were implementing the anonymous fund-with-a-bitcoin-address system, I would do something like:
Customer "Ed" gives a "send winnings to address"-- lets say it just happens to be 1Ed....
Casino gives a funding address -- lets call that address 1fundEd...
Casino creates an account named "1Ed..." and associates it with address 1fundEd.
So any coins Ed sends to 1fundEd.... go into the 1Ed... account.
When Ed wants to place a bet, casino checks to see if he has money: getbalance 1Ed....
If he does, he can place a bet.
If he wins, casino sends money:
move BANK 1Ed... <amount Ed won above his bet>
sendfrom 1Ed... 1Ed.... <amount Ed won> # Account name and cash-out address are the same.
If he loses:
move 1Ed... BANK <amount Ed lost>
listtransactions is for showing Ed a detailed list of what happened to his account.