There is no simple way Gox can make this work.
If that were true, they should make it a lot harder to shoot yourself in the foot. Like a real warning!
I'm not sure who the "they" is here. If you mean Gox, I'm not sure how much effort it is fair to require of them to work around other people's assumptions that are known to be broken.
Although, I bet it is surprisingly easy to figure out what's where from that data (just a graph traversal).
It is if you investigate it. I would analogize it to intentionally depositing money in the wrong bank account -- if some company keeps sending them money over and over addressed to the wrong account, at some point the bank has to draw the line. It's not fair to expect them to continue debiting the accounts of innocent customers incorrectly credited by someone else's mistake. It's not unreasonable for them to say that they'll credit the accounts the depositor asks them to credit rather than having to constantly tell innocent customers that their balance is wrong.