There in-lies the problem. The only way to get a complete bulletproof theory is to get MtGox to open up their information and records to be scrutinized, which, hah...yeah right.

With the info from the letstalkbitcoin action from 2011, it's about as solid as you can get that:
1. The two wallets being referred to were created by MtGox/Mark
2. On 2011-11-16 05:59:08, 40,000 bitcoin were transferred one wallet: (https://blockchain.info/address/1cXNTyXj4xPGopfYZNY5xfSM1EPJJvBZV)
3. Those 40,000 bitcoin were untouched and to this moment are still in that wallet.
4. On 2011-11-16 05:59:08, 50,000 bitcoin were transferred to the other wallet: (https://blockchain.info/address/1P3S1grZYmcqYDuaEDVDYobJ5Fx85E9fE9)
5. Those 50,000 bitcoin were untouched and to this moment are still in that wallet.

TL;DR - Pretty substantial proof MTGOX/Mark had control of those wallets when the deposits were made and the bitcoin haven't moved since.