You are assuming that the thieves stole the bitcoin and just put them into a wallet somewhere.
Consider this simplified example:
A Gox thief sold the bitcoin on another exchange. Then I unknowingly buy that very bitcoin from that exchange. Now the blockchain is rewritten and my bitcoin is gone even though I am innocent of any crime.
The MtGox situation is tragic. But when you start messing with the fungibility of bitcoin, you introduce new consequences that reach much further into the ecosystem.
I'm not making that assumption - rather the opposite, which is why I mentioned the possibility of reimbursing people later. But this isn't strictly necessary. Pragmatically, you could double spend the coins back to the original owners and then make decisions about downstream action independently. Investigation of what happened to the stolen coins might provide more clarity on the best course of action there.
Consider this simplified example:
A Gox thief sold the bitcoin on another exchange. Then I unknowingly buy that very bitcoin from that exchange. Now the blockchain is rewritten and my bitcoin is gone even though I am innocent of any crime.
The MtGox situation is tragic. But when you start messing with the fungibility of bitcoin, you introduce new consequences that reach much further into the ecosystem.