A ruling in 2010 says gay couples can amended back to 2007, but will there be penalties owed?

The only penalty that an amended return would automatically generate is for late filing if the original return was filed late provided any additional tax was paid with the return or right after you got a bill. Interest would be due on any additional tax or paid on any refund.

You would appear to have justification to request an abatement of the penalties from the FTB. Any interest involved will be collected and generally cannot be waived. That would largely be offset by interest paid by the FTB on the other amended return with the refund, so would be pretty close to a wash.

The ruling says couples CAN amend. They are not required to do so.

in Calif. those who are registered with the Sec. of State as domestic couples can file married, jointly

this does not apply to your federal return, only your Calif

no its not required