Optimizing the accounts code to add a berkeley db index table that indexed wallet transactions by account, and that cached account balances (and invalidated or updated the cache on receive/send) shouldn't be terribly hard for somebody who already knows c++ and berkeley db.
It is not on my short-term TODO list because there are too many other higher priority things on my TODO list, but a nice clean well-tested upward-compatible patch would be most welcome.
PS: for ClearCoin, I used the "bitcoind keeps track of the bitcoins" architecture, and I never regretted it-- no problems with synchronization, less possibility for MtGox-like hacks that create mythical bitcoin balances out of thin air by adding an entry to a database.