If you had 2fa enabled on btce and gmail, there should be 0 chance of anyone hacking your account. Are you sure it was enabled on both?
I only had 2FA on BTC-e not on my gmail. I just added 2FA to my gmail. As far as I know BTC-e doesn't have SMS 2FA though only 2FA via e-mail which is pointless if someone has access to your e-mail. I have heard they now have 2FA through Google Authenticator though.
They've had 2fa through gauth for quite some time now. At least a year, from what I remember. Either way, I am sorry to hear about your problems, I hope you're able to track this SOB down.