This isn't a problem bitcoin companies outgrow; it's a problem that festers as the company gets more successful. Do you go out like Flexcoin did, or like MtGox? Either way: you eventually do get taken out.
It seems that the only way for this line of business to be feasible in the long term is for the hot wallet :: total assets ratio to be as low as possible. Your income to build assets is proportional to transaction volume, but so is the required size of the hot wallet.
Maybe a massive up-front investment to allow for start-up assets to be suitably large in comparison to hot wallet size... but even then you'd need to be careful not to grow too quickly and to ensure that you proportionally build up your reserves for when your hot wallet gets wiped out.
But this means that you have those stored assets that you can't invest elsewhere, so are you even making a profit now? The only way to reduce assets needed is probably some kind of insurance arrangement, but why should the insurance company offer low fees for this with the risk profile we currently see?
Much higher levels of isolation (such as running the transaction engine in some kind of HSM) would help, but I suspect that anyone smart enough and cautious enough to do it properly is too smart and cautious to go anywhere near the prospect of running a bitcoin exchange.
Nothing in Bitcoin is reversible. Everyone working with them has to be hyper-vigilant, always, constantly, whatever you do don't blink, blink and you're dead.
I think if I were working with Bitcoins I'd get an ulcer.
For thousands of years the only way to pay for something was with non-revertible mediums, either cash or bartering for other goods. Reversible transactions are new in the grand scheme of things.
If I ran a bank and didn't bother to lock the doors or keep the money in a safe and someone comes in and steals the money, I don't get to do a chargeback and get the cash back.
That would be one thing if physical security were just as hard (or harder) than cyber security.
But it's in fact the complete and polar opposite; physical security is much easier and much better understood by the actors who need to engage in defense.
Irreversible + manual = opportunities for people to spot the fraud; volume limited by amount of work required to commit each fraud.
Reversible + automatable = opportunity to spot and undo the fraud.