Let us pretend I am in control of a wallet which holds a certain number of coins, using your example, stolen from said exchange. I also happen to own a couple of what you would consider "clean" bitcoins. To illustrate my point I choose two spend two outputs, one "clean" and one "tainted", to the same input.
Looking at said input, can you tell which satoshi is "tainted" and which is not?
the only problem is what lawyers think / do when they know that you was in control of said outputs.
Seems to me then we are deriving into the anonymity/privacy problem, are we not?
I frankly fail to see how this is an indictment on Bitcoin's fungibility.