In this case I suppose it will come down to whether the Bankruptcy Judge finds that the Bitcoins stolen at the time were of value too (and must be replaced at their market value in USD) or not.
This. I would also point out there isn't a single precedent that a judge could rely on so the judge would be essentially writing new law (something most judges don't like doing). It is likely that a judge would look for regulation of Bitcoin (and exchanges) before accepting they have value as deposits under US Bankruptcy law.
Why? Well otherwise the potential for abuse is huge.