What in the block chain says that the tainted satoshis are USD?
Do you need a centralized server from the issuers to tell you what satoshis are "tainted dollars"?
Yes, in a certain moment the server would announce new backed coins. After that, anyone can keep track of their movements. A common protocol could be defined so that different issuers can use the same software, just by adding different announcing servers.
Of course such announcement could be done in a P2P network, but there's no point in it, since the issuer is already a known central entity in which you have to trust anyway.
Yes, fees. The same incentive that miners will ask for moving tainted coins. Merged mining already exists, is working for namecoin.
Do you know why people chose to create a new, independent chain for namecoin, with coins of its own?
Why not a chain dependent on bitcoin's chain, using bitcoin themselves for the transactions?
Back to the topic, the fee structure is already there for bitcoin transactions. By creating another chain, you'd need to pay fees for both wouldn't you?