A serious problem is, even taking delivery of your bitcoins from Mt Gox, won't really protect bitcoin holders from the possibility that Mt Gox has a problem. Just look at what happened to the bitcoin market prices last summer.
I think, even if its more expensive to do complete segregation of customer funds and 100% funding of all customer deposits (in whatever currency the customer has deposited as demand deposits at highly rated banks), for Mt Gox to take that step, would be a huge service both to themselves and to the bitcoin community.
As an exchange, it's in Mt Gox's long term interest as it would enhance the sustainability of their business model--they have a vested interested that no one lose confidence in their exchange or in bitcoin in general (the latter two can't really be separated for now since Mt Gox has such a large share of the exchange market).
Short of that, a reputable CDS market for Mt Gox might help.

Or if someone would step forward some day to form a clearinghouse for settlements that operates with separation of customer deposits and full disclosure, all the exchanges could start using it.