Think of it this way.
If MtGox was a Tor based exchange, would there be any problems with it?
No, because Mark knows that Tor cannot be hacked.
So.....
You have absolutely no idea what caused the mtgox issues.
The method of reaching the servers has nothing to do with it.
Tor doesn't provide any additional security, all it does is provide anonymity.
The security of a website, their systems and their back-end is entirely unrelated to whether Tor is used or not.
If you do not understand this you're not even remotely qualified to make any comment on this subject.
All Tor would accomplish is make it even easier for the owner to run off with the coins.