Your wife has the option of filing as a resident of PA, your State of Legal Residence. Doing so would make her income not taxable by CA. See Residence of Spouse of Servicemember on page 3 of this California tax publication:
https://www.ftb.ca.gov/forms/2020/2020-1032-publication.pdf
Therefore you and your wife could choose to file a joint return in PA. Your military income would not be taxed by PA, since you're stationed outside the state. Nor is it taxable by CA.
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
