If I'm understanding correctly, the court found that he couldn't claim ownership of a particular, tangible set of bitcoins out of Mt Gox's holdings, but he's still a creditor of Mt Gox because they did owe him a specific number bitcoins.
That doesn't make any sense though unless bitcoins can be owned. If you could claim as a creditor for something that was of worth but couldn't be owned then one could say something like "I told Mt.Gox employees a joke, therefore I claim financial remuneration for the value of that experience I gave them.".
If, say, a "sell it on ebay" store went bankrupt, I could say, "those are my Air Jordans", and I would get those particular shoes back. On the other hand, if a bank goes bankrupt, I can't say "I deposited those particular bills with those serial numbers". The court has ruled that bitcoins follow the latter principle, so if each depositor gets back 50% of the deposited bitcoins, I can't get back 100% by pointing to the particular bitcoins I deposited.
If half the money is stolen from the bank vault, everyone at the bank has lost half their money (ignoring insurance, etc). If the contents of half the safe deposit boxes are stolen, you don't distribute the remaining safe deposit boxes among all the customers; half lost everything and half lost nothing.
To make the analogy to real money, if you put a stack of bills in a security deposit box in a bank, and the bank goes bankrupt, you can get the contents of the box back, because you still own those specific bills. On the other hand, if you write down the serial numbers of the bills and deposit them in a bank account, then the bank goes bankrupt, you can't go into the bank's vault and pick out the bills that match your list of serial numbers. You have to get in line with the other people who have money deposited in the bank, because you don't own those specific bills anymore.
So, basically they just decided that MtGox operates more like a bank account for bitcoins than like a security deposit box for bitcoins.
If the bank was merely holding my money in an account balance, then I could not sue in this manner since I would be treated like any other debtor in the bankruptcy proceeding.
Someone tried to sue MTGox to get their money back as if they were in the first situation. The court correctly ruled that the plaintiff was actually in the latter situation and they would have to be treated like a debtor.