To put things in perspective, nobody has seen the US government closing down and sequestrating assets and accounts of JPM or Goldman Sachs further some of their worst alleged frauds (documented, that were much worse than what is being presented to the public right now).
Therefore the way they decided to deal with the issue is highly political and meant at causing more harm than anything else. And this has a consequence on honest people, but I repeat myself.
The difference is that when you invest money with JPM or Goldman Sachs, you are investing in a financial entity that is sanctioned and regulated by the US government. The benefit to doing that is that your funds are generally protected and considered safe.
When you make the decision to move funds into BTC-E, you're on your own because you chose to go outside of the regulated system - from a practical standpoint, the US has no obligation to you or to protect your assets at that point. It's the whole reason governments regulate their financial systems.