By immediately transferring the BTC to a paper wallet address generated on a secure, offline computer, it is simply impossible to withdraw the BTC without possession of the information on that physical piece of paper. This is far more secure than any digital or two factor auth.
Edit: I notice that Coinbase does store the vast majority of their BTC in paper wallets[1]. The problem is, Coinbase still has a copy of the private keys associated with your BTC address. While this may hinder the efforts of outside attackers, there still exists a vulnerability with those employees who have access to the systems that move BTC from cold to warm storage. That's why your BTC should always reside in an address you generated yourself and solely possess the private key to.
[1] http://blog.coinbase.com/post/33197656699/coinbase-now-stori...