Pennsylvania is her state. Some states do treat a telecommuter working from outside of the state as a worker within their state (and Pennsylvania is one that does). However, California does not. So if she has had taxes withheld to California, she should get a refund for her California taxes when you file the California return.
If you are filing your Federal return as Married Filing Joint, you will file your California return jointly also, but as nonresidents. If you are living in California, then only your income will be taxed in California; hers is not. However, her income will be taxed in PA where she is living. (She can and should file Married Filing Separately in PA).
But even though her W-2 lists California, she only is taxed in California if she was physically present in the state when she worked. This is not the case, so she should get any California taxes refunded.
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