See the psychological side here:
ANYONE LOSING 500,000 BTC (more or less worth $8,500,000 USD) WOULD BE GOING APESHIT INSANE.
Anyone would be twitting about it, shouting about it, ranting about it, talking to the press, talking shit about Mt.Gox, and cursing God, the Devil, the Archangels and his own mother.
I also think that it is unlikely that one user had 500,000 BTC in one Mt Gox account. However, if it was true, I don't think that user would necessarily come forward. Think about allinvain who claims he lost 25,000 BTC to a hacker. Some sympathize with him as a victim, but a lot of the internet see him as a laughing stock for not taking proper security measures.
I think a lot of people would come forward if they lost 500,000 BTC, but I think that there are a lot more than Buddhist monks who might decide to keep their mouths shut out of embarrassment.
These three possibilities makes Mt.Gox's claims understandable, it would be humilliating and his credibility would be completely stained forever. He wouldn't be able to admit such stupid mistakes.
You argue that Mt Gox has a motive to cover up his mistakes to save face. Couldn't the same be true for the alleged user who put 500,000 BTC into one Mt Gox account?