Whether we are talking about MtGox, Ripple, TradeFortress, Bitstamp, Coinbase or bitcoins in cold storage, this is how I see things:
1. If I am the sole controller of the private key to 25 BTC, then there is no counter-party risk.
2. If I am not the sole controller of the private key for "my" 25 BTC, then what I essentially "own" is some sort of IOU and there
must be counter-party risk. I believe it is wise to ensure that I can measure what that risk actually is should I choose to use the third-party service.
Correct me if I'm wrong but that Ripple IOU exists only to do the exchange. So why is there counter party risk?
In the IOU.
Once the exchange is finished there is no risk.
If you no longer hold the IOU and instead are the sole controller of the private key to 25 BTC there is no longer any counter-party risk.