Yes I agree with you, sadly there is no real easy way to avoid exchange risk. Shapeshift is probably the most innovative exchange I can think of, yet there are still many attack vectors that you can't really avoid.
Unfortunately, Shapeshift's service doesn't support fiat currencies (which is also one of the reasons they can operate as they do). There are times when you can't hedge in altcoins; when bitcoin is dropping and altcoins are dropping harder, you need to find an exchange to hedge the fiat value of your coins. But increasingly, it seems like it's better to just weather the storm and hold for the most part.
This seems more and more important now. If an exchange does business with US customers, they need to be licensed as an MSB and do AML/KYC. Otherwise there is risk of FBI seizure...