...disables autorun to protect from a USB transfer virus, and encrypts the offline computer with a strong password to guard against physical use he is perfectly safe (provided his paper backups remain so) because the private keys to spend coins are not accessible to the outside world, period. It doesn't matter if the online computer ever gets infected. No coins can move without being signed by the encrypted offline computer.
These are really the key points for securing the offline computer, particularly disabling autorun from USB drive. Just running Linux rather than Windows on the offline computer will help, but disabling autorun should take you 90% of the rest of the way there. Encrypting the computer? Sure, if you're paranoid enough, go for it.
