The Tokyo police leak in January implied 99% of coins were lost through insider fraud, so you're probably not so far from wrong. The ongoing debate seems to revolve around whether the bitcoins were lost during the late 2011 to 2012 time frame or more recently. Those who favour the former hypothesis believe Mt. Gox only ever held a fraction of the bitcoins deposited there after that early period. They  succeeded in covering up their losses which originally had occurred either through theft or fraud.

Until the addresses of the Mt. Gox bitcoins are released by bankruptcy trustee, Nobuaki Kobayashi, so they can be traced on the blockchain then there can be little hope of knowing for certain exactly what happened. However, there is also a lot of cash missing in bank deposits. It appears that much of Mt. Gox's remaining cash when it collapsed was set aside to pay legal expenses of the bankruptcy proceeding.