The only to prevent it, is to implement the two-facotr authentication on protocol-level instead of application-level. This brings you to smartcard-authentication, or VPN solutions (using smartcard or RSA tokens)
But if they would implement that, everybody will start screaming that they have to pay for a smartcard or rsa-token...
Be honest here, how many of you would actually want to pay for that?
What you were doing is the equivalent of living your wallet in a public place unattended, and then shouting and screaming it got stolen. You are putting your bitcoin wallet on a public accessible server, you should know the risks of this by now.
Don't leave your wallet in a public place unattended, that includes your bitcoin wallet.
Let me guess, you didn't bother to encrypt your wallet either, didn't you?
Don't blame others for lack of security, if you can't even figure out your own security best practices...
But if they would implement that, everybody will start screaming that they have to pay for a smartcard or rsa-token...
Be honest here, how many of you would actually want to pay for that?
yeah, thought so...