In regards to question #1, you will need to amend her tax return and then mail in the amended return showing your filing status as Married Filing Jointly.
In regards to question #2, you have the choice to file as Married Filing Jointly for California as this could result in a more favorable tax filing.
However, you do have the option to file as Married filing separately since your spouse did not earn any income within California. You will need to determine if you want to go this route but generally filing jointly will result in a lower tax obligation.
In your input, ensure you breakout the California source income so you are only taxed on that portion of income. You will see the input to break out this income as your proceed through the state interview section.
If you decide to file separately for California, please see the link below as to how to prepare the state return as you will be filing jointly for federal purposes.
How to File MFJ for Federal but separately for state
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