I'd say at this point, of all the choices, your best one is probably MtGox. Not only have they been through security test hell, and came out on the other side with better security in place, but they've also shown that they, as a company, are willing to take a personal loss to make their users whole again.
I have to agree with you. They may of not handled it the best they could have but they handled it. They did not hide anything and told the public what they thought was going on at the moment. The deadline thing however could of been handled better. They should of set the deadline to the most amount of time it could take not the least. But they did do a great job and made sure people got there money back. I am personally waiting for them to release there merchant api to launch my bitcoin business.