Though, big money transfers are being done with marked bills, which gives the option to catch the thief.
You can catch the thief, but you can't confiscate them from a third party
if he was uninvolved and just happened to be paid with one such bills.
And you can already try to do that with bitcoin: the ledger is public and you can look at the path that those coins will follow, eventually hitting a known address.
Which might or might not be related with the thief.
It likely won't.
First, it is only an idea that I don't know how to resolve all the problems with it.
What I thought of is to block the address of the thief, that way he won't be able to pay anyone so there is no problem with confiscating money from uninvolved party.
Take the theft from MT.Gox, the addresses are known and the coins are untouched, so if miners will refuse to mine transactions from these addresses only the thief will be harmed, it won't get the coins back but it will reduce the incentive from stealing.
As I wrote before, now someone needs to find a way to prove that it is really a theft.