Advice, going forward, for managing counterparty risk:
(1) Split a $100 transaction into 10 $10* transactions executed incrementally (send $10 of BTC to Mt. Gox, exchange it, transfer it out, and only then send the next $10 of BTC over). This keeps exposure at any given time at a manageable level. The downside is it increases exposure to BTC/USD volatility.
(2) Split a $100 into 5 $20 transactions executed simultaneously on many exchanges. This keeps exposure to any single institution at a manageable level. The downside is it increases the number of institutions which must be dealt with.
(3) Draft a special arrangement with the institution for a large transaction. This should include credit and speedy withdrawal guarantees. The downside is the legal cost.
*edit: I am illustrating a hypothetical $100 transaction. Substitute, in place of $10, the most you are willing to lose in the event the exchange proves insolvent.