Yes, you can file your Federal taxes jointly and then file a separate VA state tax return for your wife. In fact,
you are required to do this.From the VA 2016 Form 760
Resident Individual Income Tax Booklet:
"Married Taxpayers: If one spouse is a Virginia resident
and the other is a nonresident, you may not file a joint
Virginia return unless you both elect to determine your
joint Virginia taxable income as if you were both Virginia
residents. If the spouses do not make such election,
the resident spouse will file either Form 760 or Form 760PY, while the nonresident spouse will filele Form
763, if applicable."
