I experienced the same issue described above, so I reopened my original federal return TurboTax file AFTER I had e-filed my federal return and it had been accepted by the IRS. I checked my filing status within TurboTax, which came back accepted, and THEN I made a copy of the file. I built my California state return in that file copy. I first changed my marital status to Married, indicating that I did NOT want to file my return together with my spouse, and then changed my filing status to Married Filing Separately. I then created and filled out my California state return. When I finished, I opted to e-file. I was ONLY offered the option to file my California state return (since TurboTax recognized I had already e-filed the federal portion), and this time around I was allowed to do so -- I did not receive the "State cannot be e-filed before your federal..." message.
