strictly philosophically, if Mt. Gox wants to question someone for coins sent to them that they recognize as originally being stolen from them, I don't see that the same thing as playing sheriff, no differently than if someone presents me cash as payment whose serial numbers I recognized as being stolen from me. If you present cash to a bank for deposit and it happens to be colored with a spray of red dye (the kind from time-delay exploding dye packs given to bank robbers), you should expect questions and not be surprised.
I also don't believe that just because Bitcoin is cash-like and often anonymous, that laws are irrelevant. In practice, Bitcoin certainly puts the law out of reach of a lot of things, but I don't think laws simply cease to apply in theory just because of that.
In the case of a bank detecting stolen serial numbers or dyed notes, the investigation will be handed over to law enforcement - the bank's role is one of informant. That's not quite the same thing as Mt Gox freezing someone's account for containing "tainted" coins. It's possible that they're exceeding their legal authority in doing that, but it's also unlikely that anyone is going to launch costly international litigation in order to have that issue determined. To a large extent, Mt Gox and the other exchanges can do whatever the fuck they want as long as it's not criminal because it's just not very likely that anyone is going to seek civil remedies against them.