If you are stationed in HI it is neither your or her home state.
Active duty service members have always been able to keep one state as their state of legal residency (usually their Home of Record) for tax purposes even when they move frequently on military orders.
Military spouses do not have a home of record. A state of legal residence, or domicile, is the place where the service member thinks of as home, the state where you intend to live after you leave the military. Your state of legal residence may change throughout your life.
Your spouse can use her resident state when filing her taxes.
However, The Military Spouse Residency Relief Act (MSRRA) allows a nonmilitary spouse of a service member to keep the same resident state of the military spouse regardless of which state they live in.
So she can choose VA or CA.
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Your non-military spouse needs to file form HW-4 with her civilian employer, so that HI state taxes are not withheld from her pay and she is not subject to paying taxes to the state of HI.
The form and instructions are at http://www.fmo.hawaii.edu/payroll/docs/Hawaii_State_Tax_Form_HW-4.pdf
Just curious, but during your in-processing briefing you received upon your arrival, were you not briefed on this? I certainly was when I first arrived in HI back in the 90's.