Precisely what did Mt. Gox do wrong?
Specifically:


They blamed transaction malleability for a hack, which was clearly a lie - blaming Bitcoin for their own mistakes.
They stopped withdrawals but continued allowing deposits and trading. A leaked strategy document shows that this was an attempt to conceal the size of their losses from the public, ie they didnt' come clean when they should have .  http://www.scribd.com/doc/209050732/MtGox-Situation-Crisis-Strategy-Draft#scribd
Their communication with their customers leading up to the hack was generally awful.