Bitcoin's transparency is one of the features that will help Bitcoin's further acceptance. The idea that criminals evade the use of Bitcoin (because transparent) could give it a further token of legitimacy.
This is completely incorrect, unfortunately. The opposite is true.
For money to be trusted, and ultimately valued, people cannot be fearful that some specific tokens within the money supply are subject to non-acceptance or seizure. Having this characteristic devalues the money properties of a given money instrument, and so Shapeshift, Changely and whoever else are working against Bitcoin's wider acceptance (and market value) by behaving in this manner.
Furthermore, Bitcoin's design exacerbates this problem: 2 or more inputs can be combined into a single output in a Bitcoin transaction. That means that blacklisted inputs can be mixed seamlessly with any number of "clean" inputs too. Doing this carefully, those that wish to make blacklisted BTC acceptable can make the job of blacklisting unworkable in practical terms.
The real solution to immoral or criminal acts is rather like that of one's health: prevention > cure.
Loss is a part of life. When you lose something or are violated somehow as a consequence of someone tricking you or taking advantage of your unawareness, it's often best to accept the loss and move on. Learning from one's mistakes (and those of others) seems to be going out of fashion since the 20th century, I expect the age of cryptocracy will re-introduce the school of hard knocks to the coddled middle-classes once again (the working class and modern elite class are much better versed in the realities of anti-social & sociopathic behaviour types, the middle class have been made overgrown schoolchildren by their over-reliance on the state)
