Right, the server might not be able to use a gui. But bitcoin-d wallets has private keys and you could run bitcoin-qt on your own pc right? The bitcoin-d account system should be able to provide a list of users that want to get their withdraw. Or the list could be taken directly form database. And it should be possible to edit the date for the account system in case you manually did a withdraw for a customer.
Wouldnt that be way less work than manually doing transactions one by one each 20-50 minutes?

And before bitcoin-qt came out there should be at least one commandline wallet that should be able to do bulk transfers too.

I see that data has to be changed back and forth but you stated already that you do such things on a small scale to do many small transactions. So it shouldnt be a big difference.