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.
I think that's part of the reason there was so much confusion in the first place with the email thread you posted. Like it's said below, someone who intentionally uses something that they know won't work isn't something that people are going to be thinking about and it'll require a lot of explanation!
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.
Agreed. If it were a large sum of money (hundreds of thousands of dollars), a reasonable person could be expected to question it, but for someone who deals in large volumes, which this other account user might be, a reasonable person may not bat an eye that their books are off by about 3 BTC (or whatever the transaction was for).