How would you get everyone to agree on the blacklisting? How would be enforced? What if some clients accept nodes containing 'blacklisted' addresses, and some don't? When if then a client that 'blacklists' addresses sees a block that contains a transaction whose inputs are 99% 'legit' coins and 1% 'blacklisted' coins? Should it honor it?

What you're really proposing is a hard fork, which is a morass of problems. And why should everyone suffer all this grief just because the security team on one exchange in Japan is staffed with people who don't know what they are doing?