I'm a strong believer that Bitcoin needs to be fungible to work. IE: all coins are equal, there's no 'dirty coins' which clients won't processes or accept.

That said, if it turns out that all of MtGox coins were stolen, and they add up to 6% of all mined coins, then it would seem we do have a little bit of a quandary. Is bitcoin really going to work if one person has 6% of all mined coins? Won't the market always be at the mercy of this individual? Perhaps not- money laundering requirements, and regulatory oversight from the government could mean that spending 6% of all coins might prove impossible for the thief, but then again, we didn't want regulation as well.

It seems like a tricky proposition to be sure.